diff --git a/docs/generated/packages/cypress/generators/component-configuration.json b/docs/generated/packages/cypress/generators/component-configuration.json
index 6fc62deecec01..2beddcaacbc1f 100644
--- a/docs/generated/packages/cypress/generators/component-configuration.json
+++ b/docs/generated/packages/cypress/generators/component-configuration.json
@@ -33,6 +33,11 @@
         "type": "string",
         "description": "A directory where the project is placed relative from the project root",
         "default": "cypress"
+      },
+      "jsx": {
+        "description": "Whether or not this project uses JSX.",
+        "type": "boolean",
+        "default": true
       }
     },
     "required": ["project"],
diff --git a/docs/generated/packages/cypress/generators/configuration.json b/docs/generated/packages/cypress/generators/configuration.json
index d9b209b8a9398..b9ae6fbe475ba 100644
--- a/docs/generated/packages/cypress/generators/configuration.json
+++ b/docs/generated/packages/cypress/generators/configuration.json
@@ -81,6 +81,11 @@
         "enum": ["vite", "webpack", "none"],
         "x-prompt": "Which Cypress bundler do you want to use?",
         "default": "webpack"
+      },
+      "jsx": {
+        "description": "Whether or not this project uses JSX.",
+        "type": "boolean",
+        "default": true
       }
     },
     "required": ["project"],
diff --git a/docs/generated/packages/cypress/generators/cypress-project.json b/docs/generated/packages/cypress/generators/cypress-project.json
index f242c0f036ef4..e5ae6e71b9724 100644
--- a/docs/generated/packages/cypress/generators/cypress-project.json
+++ b/docs/generated/packages/cypress/generators/cypress-project.json
@@ -57,12 +57,6 @@
         "description": "Whether or not to configure the ESLint `parserOptions.project` option. We do not do this by default for lint performance reasons.",
         "default": false
       },
-      "standaloneConfig": {
-        "description": "Split the project configuration into `<projectRoot>/project.json` rather than including it inside workspace.json.",
-        "type": "boolean",
-        "default": true,
-        "x-deprecated": "Nx only supports standaloneConfig"
-      },
       "skipPackageJson": {
         "type": "boolean",
         "default": false,
diff --git a/docs/generated/packages/storybook/generators/cypress-project.json b/docs/generated/packages/storybook/generators/cypress-project.json
index 11cebcf71df2e..9235f914e044c 100644
--- a/docs/generated/packages/storybook/generators/cypress-project.json
+++ b/docs/generated/packages/storybook/generators/cypress-project.json
@@ -33,12 +33,6 @@
         "enum": ["eslint", "none"],
         "default": "eslint"
       },
-      "standaloneConfig": {
-        "description": "Split the project configuration into `<projectRoot>/project.json` rather than including it inside `workspace.json`.",
-        "type": "boolean",
-        "default": true,
-        "x-deprecated": "Nx only supports standaloneConfig"
-      },
       "ciTargetName": {
         "type": "string",
         "description": "The name of the devServerTarget to use for the Cypress CI configuration. Used to control if using <storybook-project>:static-storybook:ci or <storybook-project>:storybook:ci",
@@ -49,6 +43,11 @@
         "type": "boolean",
         "default": false,
         "x-priority": "internal"
+      },
+      "projectNameAndRootFormat": {
+        "description": "Whether to generate the project name and root directory as provided (`as-provided`) or generate them composing their values and taking the configured layout into account (`derived`).",
+        "type": "string",
+        "enum": ["as-provided", "derived"]
       }
     },
     "required": ["name"],
diff --git a/packages/angular/src/generators/application/__snapshots__/application.spec.ts.snap b/packages/angular/src/generators/application/__snapshots__/application.spec.ts.snap
index f0bf73bb2bbb0..ca8234587f71e 100644
--- a/packages/angular/src/generators/application/__snapshots__/application.spec.ts.snap
+++ b/packages/angular/src/generators/application/__snapshots__/application.spec.ts.snap
@@ -369,6 +369,7 @@ exports[`app --project-name-and-root-format=derived should generate correctly wh
   "compilerOptions": {
     "allowJs": true,
     "forceConsistentCasingInFileNames": true,
+    "module": "commonjs",
     "noFallthroughCasesInSwitch": true,
     "noImplicitOverride": true,
     "noImplicitReturns": true,
@@ -383,9 +384,12 @@ exports[`app --project-name-and-root-format=derived should generate correctly wh
   },
   "extends": "../../../tsconfig.base.json",
   "include": [
-    "src/**/*.ts",
-    "src/**/*.js",
+    "**/*.ts",
+    "**/*.js",
     "cypress.config.ts",
+    "**/*.cy.ts",
+    "**/*.cy.js",
+    "**/*.d.ts",
   ],
 }
 `;
@@ -609,6 +613,7 @@ exports[`app --project-name-and-root-format=derived should generate correctly wh
   "compilerOptions": {
     "allowJs": true,
     "forceConsistentCasingInFileNames": true,
+    "module": "commonjs",
     "noFallthroughCasesInSwitch": true,
     "noImplicitOverride": true,
     "noImplicitReturns": true,
@@ -623,9 +628,12 @@ exports[`app --project-name-and-root-format=derived should generate correctly wh
   },
   "extends": "../../tsconfig.base.json",
   "include": [
-    "src/**/*.ts",
-    "src/**/*.js",
+    "**/*.ts",
+    "**/*.js",
     "cypress.config.ts",
+    "**/*.cy.ts",
+    "**/*.cy.js",
+    "**/*.d.ts",
   ],
 }
 `;
@@ -874,6 +882,7 @@ exports[`app --strict should enable strict type checking: e2e tsconfig.json 1`]
   "compilerOptions": {
     "allowJs": true,
     "forceConsistentCasingInFileNames": true,
+    "module": "commonjs",
     "noFallthroughCasesInSwitch": true,
     "noImplicitOverride": true,
     "noImplicitReturns": true,
@@ -888,9 +897,12 @@ exports[`app --strict should enable strict type checking: e2e tsconfig.json 1`]
   },
   "extends": "../tsconfig.base.json",
   "include": [
-    "src/**/*.ts",
-    "src/**/*.js",
+    "**/*.ts",
+    "**/*.js",
     "cypress.config.ts",
+    "**/*.cy.ts",
+    "**/*.cy.js",
+    "**/*.d.ts",
   ],
 }
 `;
@@ -1218,6 +1230,7 @@ exports[`app not nested should generate files: e2e tsconfig.json 1`] = `
   "compilerOptions": {
     "allowJs": true,
     "forceConsistentCasingInFileNames": true,
+    "module": "commonjs",
     "noFallthroughCasesInSwitch": true,
     "noImplicitOverride": true,
     "noImplicitReturns": true,
@@ -1232,9 +1245,12 @@ exports[`app not nested should generate files: e2e tsconfig.json 1`] = `
   },
   "extends": "../tsconfig.base.json",
   "include": [
-    "src/**/*.ts",
-    "src/**/*.js",
+    "**/*.ts",
+    "**/*.js",
     "cypress.config.ts",
+    "**/*.cy.ts",
+    "**/*.cy.js",
+    "**/*.d.ts",
   ],
 }
 `;
diff --git a/packages/angular/src/generators/application/lib/add-e2e.ts b/packages/angular/src/generators/application/lib/add-e2e.ts
index d8ddb27a991ad..545158e80ad89 100644
--- a/packages/angular/src/generators/application/lib/add-e2e.ts
+++ b/packages/angular/src/generators/application/lib/add-e2e.ts
@@ -10,23 +10,27 @@ import {
 } from '@nx/devkit';
 import { nxVersion } from '../../../utils/versions';
 import type { NormalizedSchema } from './normalized-schema';
-import { cypressProjectGenerator } from '@nx/cypress';
+import { configurationGenerator } from '@nx/cypress';
 
 export async function addE2e(tree: Tree, options: NormalizedSchema) {
   if (options.e2eTestRunner === 'cypress') {
     // TODO: This can call `@nx/web:static-config` generator when ready
     addFileServerTarget(tree, options, 'serve-static');
-
-    await cypressProjectGenerator(tree, {
-      name: options.e2eProjectName,
-      directory: options.e2eProjectRoot,
-      // the name and root are already normalized, instruct the generator to use them as is
-      projectNameAndRootFormat: 'as-provided',
-      project: options.name,
+    addProjectConfiguration(tree, options.e2eProjectName, {
+      projectType: 'application',
+      root: options.e2eProjectRoot,
+      sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
+      targets: {},
+      tags: [],
+      implicitDependencies: [options.name],
+    });
+    await configurationGenerator(tree, {
+      project: options.e2eProjectName,
+      directory: 'src',
       linter: options.linter,
-      standaloneConfig: options.standaloneConfig,
       skipPackageJson: options.skipPackageJson,
       skipFormat: true,
+      devServerTarget: `${options.name}:serve:development`,
     });
   } else if (options.e2eTestRunner === 'playwright') {
     const { configurationGenerator: playwrightConfigurationGenerator } =
@@ -35,6 +39,7 @@ export async function addE2e(tree: Tree, options: NormalizedSchema) {
         nxVersion
       );
     addProjectConfiguration(tree, options.e2eProjectName, {
+      projectType: 'application',
       root: options.e2eProjectRoot,
       sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
       targets: {},
diff --git a/packages/angular/src/generators/cypress-component-configuration/cypress-component-configuration.spec.ts b/packages/angular/src/generators/cypress-component-configuration/cypress-component-configuration.spec.ts
index 050cebf1e423f..8ab0c77dc39b5 100644
--- a/packages/angular/src/generators/cypress-component-configuration/cypress-component-configuration.spec.ts
+++ b/packages/angular/src/generators/cypress-component-configuration/cypress-component-configuration.spec.ts
@@ -13,7 +13,7 @@ import { librarySecondaryEntryPointGenerator } from '../library-secondary-entry-
 import { generateTestApplication, generateTestLibrary } from '../utils/testing';
 import { cypressComponentConfiguration } from './cypress-component-configuration';
 
-let projectGraph: ProjectGraph;
+let projectGraph: ProjectGraph = { nodes: {}, dependencies: {} };
 jest.mock('@nx/cypress/src/utils/cypress-version');
 jest.mock('@nx/devkit', () => ({
   ...jest.requireActual<any>('@nx/devkit'),
diff --git a/packages/angular/src/generators/ng-add/migrators/projects/e2e.migrator.ts b/packages/angular/src/generators/ng-add/migrators/projects/e2e.migrator.ts
index c180bb46dab47..6ad2306ab514c 100644
--- a/packages/angular/src/generators/ng-add/migrators/projects/e2e.migrator.ts
+++ b/packages/angular/src/generators/ng-add/migrators/projects/e2e.migrator.ts
@@ -337,11 +337,11 @@ export class E2eMigrator extends ProjectMigrator<SupportedTargets> {
   private async migrateCypressE2eProject(): Promise<void> {
     const oldCypressConfigFilePath = this.getOldCypressConfigFilePath();
 
+    // TODO(v18): This needs to be removed before v18 since the generator is going away.
     await cypressProjectGenerator(this.tree, {
       name: this.project.name,
       project: this.appName,
       linter: this.isProjectUsingEsLint ? Linter.EsLint : Linter.None,
-      standaloneConfig: true,
       skipFormat: true,
     });
 
diff --git a/packages/cypress/index.ts b/packages/cypress/index.ts
index b24b600a846f1..25e308c012ada 100644
--- a/packages/cypress/index.ts
+++ b/packages/cypress/index.ts
@@ -1,12 +1,17 @@
 import { configurationGenerator } from './src/generators/configuration/configuration';
 import { componentConfigurationGenerator } from './src/generators/component-configuration/component-configuration';
+import { cypressProjectGenerator as _cypressProjectGenerator } from './src/generators/cypress-project/cypress-project';
+
 export { configurationGenerator, componentConfigurationGenerator };
 
 // Maintain backwards compatibility with the old names in case community plugins used them.
-/** @deprecated Use `configurationGenerator` instead. */
+// TODO(v18): Remove old name
+/** @deprecated Use `configurationGenerator` instead. It will be removed in Nx 18. */
 export const cypressComponentConfiguration = componentConfigurationGenerator;
 
 export { configurationGenerator as cypressE2EConfigurationGenerator };
-export { cypressProjectGenerator } from './src/generators/cypress-project/cypress-project';
+// TODO(v18): Remove project generator
+/** @deprecated Add a new project and call `configurationGenerator` instead. It will be removed in Nx 18. */
+export const cypressProjectGenerator = _cypressProjectGenerator;
 export { cypressInitGenerator } from './src/generators/init/init';
 export { migrateCypressProject } from './src/generators/migrate-to-cypress-11/migrate-to-cypress-11';
diff --git a/packages/cypress/src/generators/base-setup/base-setup.ts b/packages/cypress/src/generators/base-setup/base-setup.ts
index bd0b95f70ec5a..545844875365c 100644
--- a/packages/cypress/src/generators/base-setup/base-setup.ts
+++ b/packages/cypress/src/generators/base-setup/base-setup.ts
@@ -17,6 +17,7 @@ export interface CypressBaseSetupSchema {
    * default is `cypress`
    * */
   directory?: string;
+  jsx?: boolean;
 }
 
 export function addBaseCypressSetup(
@@ -33,6 +34,7 @@ export function addBaseCypressSetup(
 
   generateFiles(tree, join(__dirname, 'files'), projectConfig.root, {
     ...opts,
+    jsx: !!opts.jsx,
     offsetFromRoot: offsetFromRoot(projectConfig.root),
     offsetFromProjectRoot: opts.hasTsConfig ? opts.offsetFromProjectRoot : '',
     tsConfigPath: opts.hasTsConfig
diff --git a/packages/cypress/src/generators/base-setup/files/__directory__/tsconfig.json b/packages/cypress/src/generators/base-setup/files/__directory__/tsconfig.json__ext__
similarity index 76%
rename from packages/cypress/src/generators/base-setup/files/__directory__/tsconfig.json
rename to packages/cypress/src/generators/base-setup/files/__directory__/tsconfig.json__ext__
index c07c6593913bc..eb50c8dd4140a 100644
--- a/packages/cypress/src/generators/base-setup/files/__directory__/tsconfig.json
+++ b/packages/cypress/src/generators/base-setup/files/__directory__/tsconfig.json__ext__
@@ -12,9 +12,9 @@
     "**/*.js",
     "<%= offsetFromProjectRoot %>cypress.config.ts",
     "<%= offsetFromProjectRoot %>**/*.cy.ts",
-    "<%= offsetFromProjectRoot %>**/*.cy.tsx",
+    <% if (jsx) { %> "<%= offsetFromProjectRoot %>**/*.cy.tsx",<% } %>
     "<%= offsetFromProjectRoot %>**/*.cy.js",
-    "<%= offsetFromProjectRoot %>**/*.cy.jsx",
+    <% if (jsx) { %>"<%= offsetFromProjectRoot %>**/*.cy.jsx",<% } %>
     "<%= offsetFromProjectRoot %>**/*.d.ts"
   ]
 }
diff --git a/packages/cypress/src/generators/component-configuration/component-configuration.spec.ts b/packages/cypress/src/generators/component-configuration/component-configuration.spec.ts
index 1934a657d7bb6..da062d1dd58a4 100644
--- a/packages/cypress/src/generators/component-configuration/component-configuration.spec.ts
+++ b/packages/cypress/src/generators/component-configuration/component-configuration.spec.ts
@@ -100,6 +100,7 @@ describe('Cypress Component Configuration', () => {
     await componentConfigurationGenerator(tree, {
       project: 'cool-lib',
       skipFormat: false,
+      jsx: true,
     });
     const projectConfig = readProjectConfiguration(tree, 'cool-lib');
     expect(tree.exists('libs/cool-lib/cypress.config.ts')).toEqual(true);
diff --git a/packages/cypress/src/generators/component-configuration/component-configuration.ts b/packages/cypress/src/generators/component-configuration/component-configuration.ts
index b8187b649c2e0..ad1a65da4fb8e 100644
--- a/packages/cypress/src/generators/component-configuration/component-configuration.ts
+++ b/packages/cypress/src/generators/component-configuration/component-configuration.ts
@@ -85,6 +85,7 @@ function addProjectFiles(
   addBaseCypressSetup(tree, {
     project: opts.project,
     directory: opts.directory,
+    jsx: opts.jsx,
   });
 
   generateFiles(
diff --git a/packages/cypress/src/generators/component-configuration/schema.d.ts b/packages/cypress/src/generators/component-configuration/schema.d.ts
index bd8ea6198ade7..4b2e26ce4275e 100644
--- a/packages/cypress/src/generators/component-configuration/schema.d.ts
+++ b/packages/cypress/src/generators/component-configuration/schema.d.ts
@@ -3,4 +3,5 @@ export interface CypressComponentConfigurationSchema {
   skipFormat: boolean;
   directory?: string;
   bundler?: 'webpack' | 'vite';
+  jsx?: boolean;
 }
diff --git a/packages/cypress/src/generators/component-configuration/schema.json b/packages/cypress/src/generators/component-configuration/schema.json
index a34fbc9d8cbd0..d7ac0b043ed81 100644
--- a/packages/cypress/src/generators/component-configuration/schema.json
+++ b/packages/cypress/src/generators/component-configuration/schema.json
@@ -31,6 +31,11 @@
       "type": "string",
       "description": "A directory where the project is placed relative from the project root",
       "default": "cypress"
+    },
+    "jsx": {
+      "description": "Whether or not this project uses JSX.",
+      "type": "boolean",
+      "default": true
     }
   },
   "required": ["project"],
diff --git a/packages/cypress/src/generators/configuration/configuration.spec.ts b/packages/cypress/src/generators/configuration/configuration.spec.ts
index 68c0ed93813eb..8d9ce68233730 100644
--- a/packages/cypress/src/generators/configuration/configuration.spec.ts
+++ b/packages/cypress/src/generators/configuration/configuration.spec.ts
@@ -52,11 +52,6 @@ describe('Cypress e2e configuration', () => {
       expect(readProjectConfiguration(tree, 'my-app').targets.e2e)
         .toMatchInlineSnapshot(`
         {
-          "configurations": {
-            "production": {
-              "devServerTarget": "my-app:serve:production",
-            },
-          },
           "executor": "@nx/cypress:cypress",
           "options": {
             "cypressConfig": "apps/my-app/cypress.config.ts",
@@ -85,9 +80,7 @@ describe('Cypress e2e configuration', () => {
             "**/*.js",
             "cypress.config.ts",
             "**/*.cy.ts",
-            "**/*.cy.tsx",
             "**/*.cy.js",
-            "**/*.cy.jsx",
             "**/*.d.ts",
           ],
         }
@@ -208,9 +201,7 @@ describe('Cypress e2e configuration', () => {
             "**/*.js",
             "../../cypress.config.ts",
             "../../**/*.cy.ts",
-            "../../**/*.cy.tsx",
             "../../**/*.cy.js",
-            "../../**/*.cy.jsx",
             "../../**/*.d.ts",
           ],
         }
diff --git a/packages/cypress/src/generators/configuration/configuration.ts b/packages/cypress/src/generators/configuration/configuration.ts
index 9c226839b86d5..31695f24a21e0 100644
--- a/packages/cypress/src/generators/configuration/configuration.ts
+++ b/packages/cypress/src/generators/configuration/configuration.ts
@@ -35,6 +35,7 @@ export interface CypressE2EConfigSchema {
   devServerTarget?: string;
   linter?: Linter;
   port?: number | 'cypress-auto';
+  jsx?: boolean;
 }
 
 type NormalizedSchema = ReturnType<typeof normalizeOptions>;
@@ -55,10 +56,12 @@ export async function configurationGenerator(
   }
   await addFiles(tree, opts);
   addTarget(tree, opts);
-  addLinterToCyProject(tree, {
+
+  const linterTask = await addLinterToCyProject(tree, {
     ...opts,
     cypressDir: opts.directory,
   });
+  tasks.push(linterTask);
 
   if (!opts.skipFormat) {
     await formatFiles(tree);
@@ -132,6 +135,7 @@ async function addFiles(tree: Tree, options: NormalizedSchema) {
     addBaseCypressSetup(tree, {
       project: options.project,
       directory: options.directory,
+      jsx: options.jsx,
     });
 
     const cyFile = joinPathFragments(projectConfig.root, 'cypress.config.ts');
@@ -197,18 +201,25 @@ function addTarget(tree: Tree, opts: NormalizedSchema) {
       port: opts.port,
     };
 
-    projectConfig.targets.e2e.configurations = {
-      [parsedTarget.configuration || 'production']: {
-        devServerTarget: `${opts.devServerTarget}${
-          parsedTarget.configuration ? '' : ':production'
-        }`,
-      },
-    };
     const devServerProjectConfig = readProjectConfiguration(
       tree,
       parsedTarget.project
     );
+    // Add production e2e target if serve target is found
+    if (
+      parsedTarget.configuration !== 'production' &&
+      devServerProjectConfig.targets?.[parsedTarget.target]?.configurations?.[
+        'production'
+      ]
+    ) {
+      projectConfig.targets.e2e.configurations ??= {};
+      projectConfig.targets.e2e.configurations['production'] = {
+        devServerTarget: `${parsedTarget.project}:${parsedTarget.target}:production`,
+      };
+    }
+    // Add ci/static e2e target if serve target is found
     if (devServerProjectConfig.targets?.['serve-static']) {
+      projectConfig.targets.e2e.configurations ??= {};
       projectConfig.targets.e2e.configurations.ci = {
         devServerTarget: `${parsedTarget.project}:serve-static`,
       };
diff --git a/packages/cypress/src/generators/configuration/schema.json b/packages/cypress/src/generators/configuration/schema.json
index 120eb500cd203..9b7025b813a88 100644
--- a/packages/cypress/src/generators/configuration/schema.json
+++ b/packages/cypress/src/generators/configuration/schema.json
@@ -84,6 +84,11 @@
       "enum": ["vite", "webpack", "none"],
       "x-prompt": "Which Cypress bundler do you want to use?",
       "default": "webpack"
+    },
+    "jsx": {
+      "description": "Whether or not this project uses JSX.",
+      "type": "boolean",
+      "default": true
     }
   },
   "required": ["project"],
diff --git a/packages/cypress/src/generators/cypress-project/schema.d.ts b/packages/cypress/src/generators/cypress-project/schema.d.ts
index 6abafe7f11c3e..d75dd885630a5 100644
--- a/packages/cypress/src/generators/cypress-project/schema.d.ts
+++ b/packages/cypress/src/generators/cypress-project/schema.d.ts
@@ -11,7 +11,6 @@ export interface Schema {
   js?: boolean;
   skipFormat?: boolean;
   setParserOptionsProject?: boolean;
-  standaloneConfig?: boolean;
   skipPackageJson?: boolean;
   bundler?: 'webpack' | 'vite' | 'none';
 }
diff --git a/packages/cypress/src/generators/cypress-project/schema.json b/packages/cypress/src/generators/cypress-project/schema.json
index 2e6b0c856e960..ba3de2c6c2b74 100644
--- a/packages/cypress/src/generators/cypress-project/schema.json
+++ b/packages/cypress/src/generators/cypress-project/schema.json
@@ -59,12 +59,6 @@
       "description": "Whether or not to configure the ESLint `parserOptions.project` option. We do not do this by default for lint performance reasons.",
       "default": false
     },
-    "standaloneConfig": {
-      "description": "Split the project configuration into `<projectRoot>/project.json` rather than including it inside workspace.json.",
-      "type": "boolean",
-      "default": true,
-      "x-deprecated": "Nx only supports standaloneConfig"
-    },
     "skipPackageJson": {
       "type": "boolean",
       "default": false,
diff --git a/packages/next/src/generators/application/lib/add-e2e.ts b/packages/next/src/generators/application/lib/add-e2e.ts
index b68e011d4fc00..15ec56c052335 100644
--- a/packages/next/src/generators/application/lib/add-e2e.ts
+++ b/packages/next/src/generators/application/lib/add-e2e.ts
@@ -12,18 +12,24 @@ import { NormalizedSchema } from './normalize-options';
 
 export async function addE2e(host: Tree, options: NormalizedSchema) {
   if (options.e2eTestRunner === 'cypress') {
-    const { cypressProjectGenerator } = ensurePackage<
+    const { configurationGenerator } = ensurePackage<
       typeof import('@nx/cypress')
     >('@nx/cypress', nxVersion);
-    return cypressProjectGenerator(host, {
+    addProjectConfiguration(host, options.e2eProjectName, {
+      root: options.e2eProjectRoot,
+      sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
+      targets: {},
+      tags: [],
+      implicitDependencies: [options.projectName],
+    });
+    return configurationGenerator(host, {
       ...options,
       linter: Linter.EsLint,
-      name: options.e2eProjectName,
-      directory: options.e2eProjectRoot,
-      // the name and root are already normalized, instruct the generator to use them as is
-      projectNameAndRootFormat: 'as-provided',
-      project: options.projectName,
+      project: options.e2eProjectName,
+      directory: 'src',
       skipFormat: true,
+      devServerTarget: `${options.projectName}:serve`,
+      jsx: true,
     });
   } else if (options.e2eTestRunner === 'playwright') {
     const { configurationGenerator } = ensurePackage<
diff --git a/packages/next/src/generators/cypress-component-configuration/cypress-component-configuration.ts b/packages/next/src/generators/cypress-component-configuration/cypress-component-configuration.ts
index eb6e972ded842..b8e6f67bdd679 100644
--- a/packages/next/src/generators/cypress-component-configuration/cypress-component-configuration.ts
+++ b/packages/next/src/generators/cypress-component-configuration/cypress-component-configuration.ts
@@ -29,6 +29,7 @@ export async function cypressComponentConfiguration(
     await baseCyCtConfig(tree, {
       project: options.project,
       skipFormat: true,
+      jsx: true,
     })
   );
 
diff --git a/packages/nuxt/src/generators/application/__snapshots__/application.spec.ts.snap b/packages/nuxt/src/generators/application/__snapshots__/application.spec.ts.snap
index 415be766b35d9..41463a5277152 100644
--- a/packages/nuxt/src/generators/application/__snapshots__/application.spec.ts.snap
+++ b/packages/nuxt/src/generators/application/__snapshots__/application.spec.ts.snap
@@ -132,14 +132,14 @@ exports[`app generated files content - as-provided should create all new files i
   "my-app/.eslintrc.json",
   "my-app/vite.config.ts",
   "my-app/tsconfig.spec.json",
-  "my-app-e2e/cypress.config.ts",
+  "my-app-e2e/project.json",
   "my-app-e2e/src/e2e/app.cy.ts",
-  "my-app-e2e/src/fixtures/example.json",
   "my-app-e2e/src/support/app.po.ts",
-  "my-app-e2e/src/support/commands.ts",
   "my-app-e2e/src/support/e2e.ts",
+  "my-app-e2e/src/fixtures/example.json",
+  "my-app-e2e/src/support/commands.ts",
+  "my-app-e2e/cypress.config.ts",
   "my-app-e2e/tsconfig.json",
-  "my-app-e2e/project.json",
   "my-app-e2e/.eslintrc.json",
 ]
 `;
diff --git a/packages/nuxt/src/generators/application/lib/add-e2e.ts b/packages/nuxt/src/generators/application/lib/add-e2e.ts
index 54bd212c35da8..d9e53e853c72d 100644
--- a/packages/nuxt/src/generators/application/lib/add-e2e.ts
+++ b/packages/nuxt/src/generators/application/lib/add-e2e.ts
@@ -12,17 +12,25 @@ import { NormalizedSchema } from '../schema';
 
 export async function addE2e(host: Tree, options: NormalizedSchema) {
   if (options.e2eTestRunner === 'cypress') {
-    const { cypressProjectGenerator } = ensurePackage<
+    const { configurationGenerator } = ensurePackage<
       typeof import('@nx/cypress')
     >('@nx/cypress', nxVersion);
-    return cypressProjectGenerator(host, {
+    addProjectConfiguration(host, options.e2eProjectName, {
+      projectType: 'application',
+      root: options.e2eProjectRoot,
+      sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
+      targets: {},
+      tags: [],
+      implicitDependencies: [options.projectName],
+    });
+    return await configurationGenerator(host, {
       ...options,
-      linter: Linter.EsLint,
-      name: options.e2eProjectName,
-      directory: options.e2eProjectRoot,
-      projectNameAndRootFormat: 'as-provided',
-      project: options.projectName,
+      project: options.e2eProjectName,
+      directory: 'src',
+      bundler: 'vite',
       skipFormat: true,
+      devServerTarget: `${options.projectName}:serve`,
+      jsx: true,
     });
   } else if (options.e2eTestRunner === 'playwright') {
     const { configurationGenerator } = ensurePackage<
diff --git a/packages/react/src/generators/application/application.spec.ts b/packages/react/src/generators/application/application.spec.ts
index 10e91148bb87e..b25be440359fc 100644
--- a/packages/react/src/generators/application/application.spec.ts
+++ b/packages/react/src/generators/application/application.spec.ts
@@ -143,6 +143,7 @@ describe('app', () => {
         {
           "compilerOptions": {
             "allowJs": true,
+            "module": "commonjs",
             "outDir": "../dist/out-tsc",
             "sourceMap": false,
             "types": [
@@ -152,9 +153,14 @@ describe('app', () => {
           },
           "extends": "../tsconfig.base.json",
           "include": [
-            "src/**/*.ts",
-            "src/**/*.js",
+            "**/*.ts",
+            "**/*.js",
             "cypress.config.ts",
+            "**/*.cy.ts",
+            "**/*.cy.tsx",
+            "**/*.cy.js",
+            "**/*.cy.jsx",
+            "**/*.d.ts",
           ],
         }
       `);
diff --git a/packages/react/src/generators/application/lib/add-e2e.ts b/packages/react/src/generators/application/lib/add-e2e.ts
index ad63dedf74c64..838fe4ce03ea7 100644
--- a/packages/react/src/generators/application/lib/add-e2e.ts
+++ b/packages/react/src/generators/application/lib/add-e2e.ts
@@ -15,31 +15,42 @@ export async function addE2e(
   options: NormalizedSchema
 ): Promise<GeneratorCallback> {
   switch (options.e2eTestRunner) {
-    case 'cypress':
+    case 'cypress': {
       webStaticServeGenerator(tree, {
         buildTarget: `${options.projectName}:build`,
         targetName: 'serve-static',
       });
 
-      const { cypressProjectGenerator } = ensurePackage<
+      const { configurationGenerator } = ensurePackage<
         typeof import('@nx/cypress')
       >('@nx/cypress', nxVersion);
 
-      return await cypressProjectGenerator(tree, {
+      addProjectConfiguration(tree, options.e2eProjectName, {
+        projectType: 'application',
+        root: options.e2eProjectRoot,
+        sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
+        targets: {},
+        implicitDependencies: [options.projectName],
+        tags: [],
+      });
+
+      return await configurationGenerator(tree, {
         ...options,
-        name: options.e2eProjectName,
-        directory: options.e2eProjectRoot,
+        project: options.e2eProjectName,
+        directory: 'src',
         // the name and root are already normalized, instruct the generator to use them as is
-        projectNameAndRootFormat: 'as-provided',
-        project: options.projectName,
         bundler: options.bundler === 'rspack' ? 'webpack' : options.bundler,
         skipFormat: true,
+        devServerTarget: `${options.projectName}:serve`,
+        jsx: true,
       });
-    case 'playwright':
+    }
+    case 'playwright': {
       const { configurationGenerator } = ensurePackage<
         typeof import('@nx/playwright')
       >('@nx/playwright', nxVersion);
       addProjectConfiguration(tree, options.e2eProjectName, {
+        projectType: 'application',
         root: options.e2eProjectRoot,
         sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
         targets: {},
@@ -58,6 +69,7 @@ export async function addE2e(
         }`,
         webServerAddress: 'http://localhost:4200',
       });
+    }
     case 'none':
     default:
       return () => {};
diff --git a/packages/react/src/generators/cypress-component-configuration/cypress-component-configuration.ts b/packages/react/src/generators/cypress-component-configuration/cypress-component-configuration.ts
index 761ca09d80d13..a756d1aeac202 100644
--- a/packages/react/src/generators/cypress-component-configuration/cypress-component-configuration.ts
+++ b/packages/react/src/generators/cypress-component-configuration/cypress-component-configuration.ts
@@ -25,6 +25,7 @@ export async function cypressComponentConfigGenerator(
   const installTask = await baseCyCtConfig(tree, {
     project: options.project,
     skipFormat: true,
+    jsx: true,
   });
 
   const found = await addCTTargetWithBuildTarget(tree, {
diff --git a/packages/storybook/src/generators/cypress-project/cypress-project.spec.ts b/packages/storybook/src/generators/cypress-project/cypress-project.spec.ts
index 3365702123f05..8b5f3ffcd6e47 100644
--- a/packages/storybook/src/generators/cypress-project/cypress-project.spec.ts
+++ b/packages/storybook/src/generators/cypress-project/cypress-project.spec.ts
@@ -1,19 +1,13 @@
-import { installedCypressVersion } from '@nx/cypress/src/utils/cypress-version';
 import { readJson, readProjectConfiguration, Tree } from '@nx/devkit';
 import { createTreeWithEmptyWorkspace } from '@nx/devkit/testing';
 import { Linter } from '@nx/eslint';
 import { libraryGenerator } from '@nx/js';
 import { cypressProjectGenerator } from './cypress-project';
 
-jest.mock('@nx/cypress/src/utils/cypress-version');
 describe('@nx/storybook:cypress-project', () => {
   let tree: Tree;
-  let mockedInstalledCypressVersion: jest.Mock<
-    ReturnType<typeof installedCypressVersion>
-  > = installedCypressVersion as never;
 
   beforeEach(async () => {
-    mockedInstalledCypressVersion.mockReturnValue(10);
     tree = createTreeWithEmptyWorkspace({ layout: 'apps-libs' });
     await libraryGenerator(tree, {
       name: 'test-ui-lib',
@@ -36,19 +30,6 @@ describe('@nx/storybook:cypress-project', () => {
     expect(cypressConfig).toMatchSnapshot();
   });
 
-  it('should update cypress.json file if present', async () => {
-    mockedInstalledCypressVersion.mockReturnValue(9);
-
-    await cypressProjectGenerator(tree, {
-      name: 'test-ui-lib',
-      linter: Linter.EsLint,
-    });
-
-    expect(tree.exists('apps/test-ui-lib-e2e/cypress.json')).toBeTruthy();
-    const cypressConfig = readJson(tree, 'apps/test-ui-lib-e2e/cypress.json');
-    expect(cypressConfig.baseUrl).toEqual('http://localhost:4400');
-  });
-
   it('should update `angular.json` file', async () => {
     await cypressProjectGenerator(tree, {
       name: 'test-ui-lib',
diff --git a/packages/storybook/src/generators/cypress-project/cypress-project.ts b/packages/storybook/src/generators/cypress-project/cypress-project.ts
index 0b7246091cf4d..a6ad8e1c231bc 100644
--- a/packages/storybook/src/generators/cypress-project/cypress-project.ts
+++ b/packages/storybook/src/generators/cypress-project/cypress-project.ts
@@ -1,15 +1,11 @@
+import { getE2eProjectName } from '@nx/cypress/src/utils/project-name';
 import {
-  cypressInitGenerator as _cypressInitGenerator,
-  cypressProjectGenerator as _cypressProjectGenerator,
-} from '@nx/cypress';
-import {
-  getE2eProjectName,
-  getUnscopedLibName,
-} from '@nx/cypress/src/utils/project-name';
-import {
+  addProjectConfiguration,
+  ensurePackage,
   formatFiles,
   generateFiles,
   GeneratorCallback,
+  joinPathFragments,
   readJson,
   readProjectConfiguration,
   runTasksInSerial,
@@ -18,9 +14,11 @@ import {
   updateProjectConfiguration,
 } from '@nx/devkit';
 import { Linter } from '@nx/eslint';
-
+import { determineProjectNameAndRootOptions } from '@nx/devkit/src/generators/project-name-and-root-utils';
 import { join } from 'path';
+
 import { safeFileDelete } from '../../utils/utilities';
+import { nxVersion } from '../../utils/versions';
 
 export interface CypressConfigureSchema {
   name: string;
@@ -30,31 +28,61 @@ export interface CypressConfigureSchema {
   standaloneConfig?: boolean;
   ciTargetName?: string;
   skipFormat?: boolean;
+  projectNameAndRootFormat?: 'as-provided' | 'derived';
 }
 
 export async function cypressProjectGenerator(
   tree: Tree,
   schema: CypressConfigureSchema
 ) {
+  return await cypressProjectGeneratorInternal(tree, {
+    projectNameAndRootFormat: 'derived',
+    ...schema,
+  });
+}
+
+export async function cypressProjectGeneratorInternal(
+  tree: Tree,
+  schema: CypressConfigureSchema
+) {
+  const { configurationGenerator, cypressInitGenerator } = ensurePackage<
+    typeof import('@nx/cypress')
+  >('@nx/cypress', nxVersion);
+
+  const e2eName = schema.name ? `${schema.name}-e2e` : undefined;
+  const { projectName, projectRoot } = await determineProjectNameAndRootOptions(
+    tree,
+    {
+      name: e2eName,
+      projectType: 'application',
+      directory: schema.directory,
+      projectNameAndRootFormat: schema.projectNameAndRootFormat,
+      callingGenerator: '@nx/storybook:cypress-project',
+    }
+  );
   const libConfig = readProjectConfiguration(tree, schema.name);
   const libRoot = libConfig.root;
-  const cypressProjectName = `${
-    schema.directory ? getUnscopedLibName(libRoot) : schema.name
-  }-e2e`;
 
   const tasks: GeneratorCallback[] = [];
 
   if (!projectAlreadyHasCypress(tree)) {
-    tasks.push(await _cypressInitGenerator(tree, {}));
+    tasks.push(await cypressInitGenerator(tree, {}));
   }
 
-  const installTask = await _cypressProjectGenerator(tree, {
-    name: cypressProjectName,
-    project: schema.name,
+  addProjectConfiguration(tree, projectName, {
+    root: projectRoot,
+    projectType: 'application',
+    sourceRoot: joinPathFragments(projectRoot, 'src'),
+    targets: {},
+    implicitDependencies: [projectName],
+  });
+
+  const installTask = await configurationGenerator(tree, {
+    project: projectName,
     js: schema.js,
     linter: schema.linter,
-    directory: schema.directory,
-    standaloneConfig: schema.standaloneConfig,
+    directory: projectRoot,
+    devServerTarget: `${schema.name}:storybook`,
     skipFormat: true,
   });
   tasks.push(installTask);
diff --git a/packages/storybook/src/generators/cypress-project/schema.json b/packages/storybook/src/generators/cypress-project/schema.json
index 1a5e689a2f770..15a6bb70c94cd 100644
--- a/packages/storybook/src/generators/cypress-project/schema.json
+++ b/packages/storybook/src/generators/cypress-project/schema.json
@@ -33,12 +33,6 @@
       "enum": ["eslint", "none"],
       "default": "eslint"
     },
-    "standaloneConfig": {
-      "description": "Split the project configuration into `<projectRoot>/project.json` rather than including it inside `workspace.json`.",
-      "type": "boolean",
-      "default": true,
-      "x-deprecated": "Nx only supports standaloneConfig"
-    },
     "ciTargetName": {
       "type": "string",
       "description": "The name of the devServerTarget to use for the Cypress CI configuration. Used to control if using <storybook-project>:static-storybook:ci or <storybook-project>:storybook:ci",
@@ -49,6 +43,11 @@
       "type": "boolean",
       "default": false,
       "x-priority": "internal"
+    },
+    "projectNameAndRootFormat": {
+      "description": "Whether to generate the project name and root directory as provided (`as-provided`) or generate them composing their values and taking the configured layout into account (`derived`).",
+      "type": "string",
+      "enum": ["as-provided", "derived"]
     }
   },
   "required": ["name"]
diff --git a/packages/vue/src/generators/application/lib/add-e2e.ts b/packages/vue/src/generators/application/lib/add-e2e.ts
index 1977289b3cc62..454273847e95d 100644
--- a/packages/vue/src/generators/application/lib/add-e2e.ts
+++ b/packages/vue/src/generators/application/lib/add-e2e.ts
@@ -15,30 +15,39 @@ export async function addE2e(
   options: NormalizedSchema
 ): Promise<GeneratorCallback> {
   switch (options.e2eTestRunner) {
-    case 'cypress':
+    case 'cypress': {
       webStaticServeGenerator(tree, {
         buildTarget: `${options.projectName}:build`,
         targetName: 'serve-static',
       });
 
-      const { cypressProjectGenerator } = ensurePackage<
+      const { configurationGenerator } = ensurePackage<
         typeof import('@nx/cypress')
       >('@nx/cypress', nxVersion);
-
-      return await cypressProjectGenerator(tree, {
+      addProjectConfiguration(tree, options.e2eProjectName, {
+        projectType: 'application',
+        root: options.e2eProjectRoot,
+        sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
+        targets: {},
+        tags: [],
+        implicitDependencies: [options.projectName],
+      });
+      return await configurationGenerator(tree, {
         ...options,
-        name: options.e2eProjectName,
-        directory: options.e2eProjectRoot,
-        projectNameAndRootFormat: 'as-provided',
-        project: options.projectName,
+        project: options.e2eProjectName,
+        directory: 'src',
         bundler: 'vite',
         skipFormat: true,
+        devServerTarget: `${options.projectName}:serve`,
+        jsx: true,
       });
-    case 'playwright':
+    }
+    case 'playwright': {
       const { configurationGenerator } = ensurePackage<
         typeof import('@nx/playwright')
       >('@nx/playwright', nxVersion);
       addProjectConfiguration(tree, options.e2eProjectName, {
+        projectType: 'application',
         root: options.e2eProjectRoot,
         sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
         targets: {},
@@ -57,6 +66,7 @@ export async function addE2e(
         }`,
         webServerAddress: 'http://localhost:4200',
       });
+    }
     case 'none':
     default:
       return () => {};
diff --git a/packages/web/src/generators/application/application.spec.ts b/packages/web/src/generators/application/application.spec.ts
index 1a12bf5790777..3f89a33c022d3 100644
--- a/packages/web/src/generators/application/application.spec.ts
+++ b/packages/web/src/generators/application/application.spec.ts
@@ -86,6 +86,7 @@ describe('app', () => {
         {
           "compilerOptions": {
             "allowJs": true,
+            "module": "commonjs",
             "outDir": "../dist/out-tsc",
             "sourceMap": false,
             "types": [
@@ -95,9 +96,12 @@ describe('app', () => {
           },
           "extends": "../tsconfig.base.json",
           "include": [
-            "src/**/*.ts",
-            "src/**/*.js",
+            "**/*.ts",
+            "**/*.js",
             "cypress.config.ts",
+            "**/*.cy.ts",
+            "**/*.cy.js",
+            "**/*.d.ts",
           ],
         }
       `);
diff --git a/packages/web/src/generators/application/application.ts b/packages/web/src/generators/application/application.ts
index 601881e2dd9a8..df6840adb06df 100644
--- a/packages/web/src/generators/application/application.ts
+++ b/packages/web/src/generators/application/application.ts
@@ -6,7 +6,6 @@ import {
   generateFiles,
   GeneratorCallback,
   getPackageManagerCommand,
-  getWorkspaceLayout,
   joinPathFragments,
   names,
   offsetFromRoot,
@@ -282,16 +281,22 @@ export async function applicationGeneratorInternal(host: Tree, schema: Schema) {
   }
 
   if (options.e2eTestRunner === 'cypress') {
-    const { cypressProjectGenerator } = ensurePackage<
+    const { configurationGenerator } = ensurePackage<
       typeof import('@nx/cypress')
     >('@nx/cypress', nxVersion);
-    const cypressTask = await cypressProjectGenerator(host, {
+    addProjectConfiguration(host, options.e2eProjectName, {
+      root: options.e2eProjectRoot,
+      sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),
+      projectType: 'application',
+      targets: {},
+      tags: [],
+      implicitDependencies: [options.projectName],
+    });
+    const cypressTask = await configurationGenerator(host, {
       ...options,
-      name: options.e2eProjectName,
-      directory: options.e2eProjectRoot,
-      // the name and root are already normalized, instruct the generator to use them as is
-      projectNameAndRootFormat: 'as-provided',
-      project: options.projectName,
+      project: options.e2eProjectName,
+      devServerTarget: `${options.projectName}:serve`,
+      directory: 'src',
       skipFormat: true,
     });
     tasks.push(cypressTask);
@@ -299,7 +304,6 @@ export async function applicationGeneratorInternal(host: Tree, schema: Schema) {
     const { configurationGenerator: playwrightConfigGenerator } = ensurePackage<
       typeof import('@nx/playwright')
     >('@nx/playwright', nxVersion);
-
     addProjectConfiguration(host, options.e2eProjectName, {
       root: options.e2eProjectRoot,
       sourceRoot: joinPathFragments(options.e2eProjectRoot, 'src'),