diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8d420e32fd..297298603d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,8 @@ This is the log of notable changes to EAS CLI and related packages.
 
 ### 🐛 Bug fixes
 
+- Avoid merging `expo.extra` plugin-generated data with `expo.extra.eas.projectId` in `eas init`. ([#2554](https://github.com/expo/eas-cli/pull/2554) by [@byCedric](https://github.com/byCedric)))
+
 ### 🧹 Chores
 
 - Make error message for invalid CFBundleShortVersionString more descriptive and actionable. Improve CFBundleShortVersionString validation regex. ([#2542](https://github.com/expo/eas-cli/pull/2542) by [@szdziedzic](https://github.com/szdziedzic))
diff --git a/packages/eas-cli/src/commandUtils/context/contextUtils/getProjectIdAsync.ts b/packages/eas-cli/src/commandUtils/context/contextUtils/getProjectIdAsync.ts
index 031aa5552e..da8d13dceb 100644
--- a/packages/eas-cli/src/commandUtils/context/contextUtils/getProjectIdAsync.ts
+++ b/packages/eas-cli/src/commandUtils/context/contextUtils/getProjectIdAsync.ts
@@ -18,13 +18,15 @@ import { Actor, getActorUsername } from '../../../user/User';
  * Save an EAS project ID to the appropriate field in the app config.
  *
  * @deprecated Should not be used outside of context functions except in the init command.
+ * @deprecated Starting from `@expo/config` from SDK 52, the `modifyConfigAsync` function is merging existing data. Once this is released, we can use that instead of manually merging.
  */
 export async function saveProjectIdToAppConfigAsync(
   projectDir: string,
   projectId: string,
   options: { env?: Env } = {}
 ): Promise<void> {
-  const exp = getPrivateExpoConfig(projectDir, options);
+  // NOTE(cedric): we disable plugins to avoid writing plugin-generated content to `expo.extra`
+  const exp = getPrivateExpoConfig(projectDir, { skipPlugins: true, ...options });
   const result = await createOrModifyExpoConfigAsync(
     projectDir,
     {
diff --git a/packages/eas-cli/src/project/expoConfig.ts b/packages/eas-cli/src/project/expoConfig.ts
index d4225f7349..aa7223b5d7 100644
--- a/packages/eas-cli/src/project/expoConfig.ts
+++ b/packages/eas-cli/src/project/expoConfig.ts
@@ -18,6 +18,7 @@ export type PublicExpoConfig = Omit<
 export interface ExpoConfigOptions {
   env?: Env;
   skipSDKVersionRequirement?: boolean;
+  skipPlugins?: boolean;
 }
 
 interface ExpoConfigOptionsInternal extends ExpoConfigOptions {
@@ -52,6 +53,7 @@ function getExpoConfigInternal(
     const { exp } = getConfig(projectDir, {
       skipSDKVersionRequirement: true,
       ...(opts.isPublicConfig ? { isPublicConfig: true } : {}),
+      ...(opts.skipPlugins ? { skipPlugins: true } : {}),
     });
 
     const { error } = MinimalAppConfigSchema.validate(exp, {