diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts
index 8c908ecc9ef87..4999c07a2aec1 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts
@@ -261,9 +261,10 @@ const installTransformsAssets = async (
     await Promise.all(
       destinationIndexTemplates
         .map((destinationIndexTemplate) => {
-          const customMappings = transformsSpecifications
-            .get(destinationIndexTemplate.transformModuleId)
-            ?.get('mappings');
+          const customMappings =
+            transformsSpecifications
+              .get(destinationIndexTemplate.transformModuleId)
+              ?.get('mappings') ?? {};
           const registryElasticsearch: RegistryElasticsearch = {
             'index_template.settings': destinationIndexTemplate.template.settings,
             'index_template.mappings': destinationIndexTemplate.template.mappings,
diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/transform.test.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/legacy_transforms.test.ts
similarity index 99%
rename from x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/transform.test.ts
rename to x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/legacy_transforms.test.ts
index 97fa1e94ca218..124004dee94ac 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/transform.test.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/legacy_transforms.test.ts
@@ -37,7 +37,7 @@ import { PACKAGES_SAVED_OBJECT_TYPE } from '../../../../constants';
 import { getAsset } from './common';
 import { installTransforms } from './install';
 
-describe('test transform install', () => {
+describe('test transform install with legacy schema', () => {
   let esClient: ReturnType<typeof elasticsearchClientMock.createElasticsearchClient>;
   let savedObjectsClient: jest.Mocked<SavedObjectsClientContract>;
   beforeEach(() => {
diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/transforms.tests.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/transforms.tests.ts
new file mode 100644
index 0000000000000..aeeeb59e12b38
--- /dev/null
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/transforms.tests.ts
@@ -0,0 +1,672 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License
+ * 2.0; you may not use this file except in compliance with the Elastic License
+ * 2.0.
+ */
+
+// eslint-disable-next-line import/order
+import { createAppContextStartContractMock } from '../../../../mocks';
+
+jest.mock('../../packages/get', () => {
+  return { getInstallation: jest.fn(), getInstallationObject: jest.fn() };
+});
+
+jest.mock('./common', () => {
+  return {
+    getAsset: jest.fn(),
+  };
+});
+
+import type { SavedObject, SavedObjectsClientContract } from '@kbn/core/server';
+import { loggerMock } from '@kbn/logging-mocks';
+
+import { savedObjectsClientMock } from '@kbn/core/server/mocks';
+import { elasticsearchClientMock } from '@kbn/core-elasticsearch-client-server-mocks';
+
+import { getInstallation, getInstallationObject } from '../../packages';
+import type { Installation, RegistryPackage } from '../../../../types';
+import { ElasticsearchAssetType } from '../../../../types';
+import { appContextService } from '../../../app_context';
+
+import { PACKAGES_SAVED_OBJECT_TYPE } from '../../../../constants';
+
+import { getESAssetMetadata } from '../meta';
+
+import { installTransforms } from './install';
+import { getAsset } from './common';
+
+const meta = getESAssetMetadata({ packageName: 'endpoint' });
+
+describe('test transform install', () => {
+  let esClient: ReturnType<typeof elasticsearchClientMock.createElasticsearchClient>;
+  let savedObjectsClient: jest.Mocked<SavedObjectsClientContract>;
+
+  const getYamlTestData = (autoStart: boolean | undefined = undefined) => {
+    const start =
+      autoStart === undefined
+        ? ''
+        : `
+start: ${autoStart}`;
+    return {
+      MANIFEST:
+        `destination_index_template:
+  settings:
+    index:
+      codec: best_compression
+      refresh_interval: 5s
+      number_of_shards: 1
+      number_of_routing_shards: 30
+      hidden: true
+  mappings:
+    dynamic: false
+    _meta: {}
+    dynamic_templates:
+      - strings_as_keyword:
+          match_mapping_type: string
+          mapping:
+            ignore_above: 1024
+            type: keyword
+    date_detection: false` + start,
+      TRANSFORM: `source:
+  index:
+    - metrics-endpoint.metadata_current_default*
+    - ".fleet-agents*"
+dest:
+  index: ".metrics-endpoint.metadata_united_default"
+frequency: 1s
+sync:
+  time:
+    delay: 4s
+    field: updated_at
+pivot:
+  aggs:
+    united:
+      scripted_metric:
+        init_script: state.docs = []
+        map_script: state.docs.add(new HashMap(params['_source']))
+        combine_script: return state.docs
+        reduce_script: def ret = new HashMap(); for (s in states) { for (d in s) { if (d.containsKey('Endpoint')) { ret.endpoint = d } else { ret.agent = d } }} return ret
+  group_by:
+    agent.id:
+      terms:
+        field: agent.id
+description: Merges latest endpoint and Agent metadata documents.
+_meta:
+  managed: true`,
+      FIELDS: `- name: '@timestamp'
+  type: date
+- name: updated_at
+  type: alias
+  path: event.ingested`,
+    };
+  };
+  const getExpectedData = () => {
+    return {
+      TRANSFORM: {
+        transform_id: 'logs-endpoint.metadata_current-default-0.16.0-dev.0',
+        defer_validation: true,
+        body: {
+          description: 'Merges latest endpoint and Agent metadata documents.',
+          dest: {
+            index: '.metrics-endpoint.metadata_united_default',
+          },
+          frequency: '1s',
+          pivot: {
+            aggs: {
+              united: {
+                scripted_metric: {
+                  combine_script: 'return state.docs',
+                  init_script: 'state.docs = []',
+                  map_script: "state.docs.add(new HashMap(params['_source']))",
+                  reduce_script:
+                    "def ret = new HashMap(); for (s in states) { for (d in s) { if (d.containsKey('Endpoint')) { ret.endpoint = d } else { ret.agent = d } }} return ret",
+                },
+              },
+            },
+            group_by: {
+              'agent.id': {
+                terms: {
+                  field: 'agent.id',
+                },
+              },
+            },
+          },
+          source: {
+            index: ['metrics-endpoint.metadata_current_default*', '.fleet-agents*'],
+          },
+          sync: {
+            time: {
+              delay: '4s',
+              field: 'updated_at',
+            },
+          },
+          _meta: meta,
+        },
+      },
+    };
+  };
+
+  beforeEach(() => {
+    appContextService.start(createAppContextStartContractMock());
+    esClient = elasticsearchClientMock.createClusterClient().asInternalUser;
+    (getInstallation as jest.MockedFunction<typeof getInstallation>).mockReset();
+    (getInstallationObject as jest.MockedFunction<typeof getInstallationObject>).mockReset();
+    savedObjectsClient = savedObjectsClientMock.create();
+    savedObjectsClient.update.mockImplementation(async (type, id, attributes) => ({
+      type: PACKAGES_SAVED_OBJECT_TYPE,
+      id: 'endpoint',
+      attributes,
+      references: [],
+    }));
+  });
+
+  afterEach(() => {
+    jest.clearAllMocks();
+  });
+
+  test('can install new versions and removes older version when start is not defined', async () => {
+    const sourceData = getYamlTestData();
+    const expectedData = getExpectedData();
+
+    const previousInstallation: Installation = {
+      installed_es: [
+        {
+          id: 'metrics-endpoint.policy-0.16.0-dev.0',
+          type: ElasticsearchAssetType.ingestPipeline,
+        },
+        {
+          id: 'endpoint.metadata_current-default-0.15.0-dev.0',
+          type: ElasticsearchAssetType.transform,
+        },
+      ],
+    } as unknown as Installation;
+
+    const currentInstallation: Installation = {
+      installed_es: [
+        {
+          id: 'metrics-endpoint.policy-0.16.0-dev.0',
+          type: ElasticsearchAssetType.ingestPipeline,
+        },
+        {
+          id: 'endpoint.metadata_current-default-0.15.0-dev.0',
+          type: ElasticsearchAssetType.transform,
+        },
+        {
+          id: 'endpoint.metadata_current-default-0.16.0-dev.0',
+          type: ElasticsearchAssetType.transform,
+        },
+        {
+          id: 'endpoint.metadata-default-0.16.0-dev.0',
+          type: ElasticsearchAssetType.transform,
+        },
+      ],
+    } as unknown as Installation;
+    (getAsset as jest.MockedFunction<typeof getAsset>)
+      .mockReturnValueOnce(Buffer.from(sourceData.MANIFEST, 'utf8'))
+      .mockReturnValueOnce(Buffer.from(sourceData.TRANSFORM, 'utf8'));
+
+    (getInstallation as jest.MockedFunction<typeof getInstallation>)
+      .mockReturnValueOnce(Promise.resolve(previousInstallation))
+      .mockReturnValueOnce(Promise.resolve(currentInstallation));
+
+    (
+      getInstallationObject as jest.MockedFunction<typeof getInstallationObject>
+    ).mockReturnValueOnce(
+      Promise.resolve({
+        attributes: {
+          installed_es: previousInstallation.installed_es,
+        },
+      } as unknown as SavedObject<Installation>)
+    );
+
+    // Mock transform from old version
+    esClient.transform.getTransform.mockResponseOnce({
+      count: 1,
+      transforms: [
+        // @ts-expect-error incomplete data
+        {
+          dest: {
+            index: 'mock-old-destination-index',
+          },
+        },
+      ],
+    });
+
+    await installTransforms(
+      {
+        name: 'endpoint',
+        version: '0.16.0-dev.0',
+      } as unknown as RegistryPackage,
+      [
+        'endpoint-0.16.0-dev.0/elasticsearch/transform/metadata_current/manifest.yml',
+        'endpoint-0.16.0-dev.0/elasticsearch/transform/metadata_current/transform.yml',
+      ],
+      esClient,
+      savedObjectsClient,
+      loggerMock.create(),
+      previousInstallation.installed_es
+    );
+
+    expect(esClient.transform.getTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'endpoint.metadata_current-default-0.15.0-dev.0',
+        },
+        { ignore: [404] },
+      ],
+    ]);
+    // Stop and delete previously installed transforms
+    expect(esClient.transform.stopTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'endpoint.metadata_current-default-0.15.0-dev.0',
+          force: true,
+        },
+        { ignore: [404] },
+      ],
+    ]);
+    expect(esClient.transform.deleteTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'endpoint.metadata_current-default-0.15.0-dev.0',
+          force: true,
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Delete destination index
+    expect(esClient.transport.request.mock.calls).toEqual([
+      [
+        {
+          method: 'DELETE',
+          path: '/mock-old-destination-index',
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Create a @package component template and an empty @custom component template
+    expect(esClient.cluster.putComponentTemplate.mock.calls).toEqual([
+      [
+        {
+          body: {
+            _meta: meta,
+            template: {
+              mappings: {
+                _meta: {},
+                date_detection: false,
+                dynamic: false,
+                dynamic_templates: [
+                  {
+                    strings_as_keyword: {
+                      mapping: { ignore_above: 1024, type: 'keyword' },
+                      match_mapping_type: 'string',
+                    },
+                  },
+                ],
+                properties: {},
+              },
+              settings: {
+                index: {
+                  codec: 'best_compression',
+                  hidden: true,
+                  mapping: { total_fields: { limit: '10000' } },
+                  number_of_routing_shards: 30,
+                  number_of_shards: 1,
+                  refresh_interval: '5s',
+                },
+              },
+            },
+          },
+          create: false,
+          name: 'logs-endpoint.metadata_current-template@package',
+        },
+        { ignore: [404] },
+      ],
+      [
+        {
+          body: {
+            _meta: meta,
+            template: { settings: {} },
+          },
+          create: true,
+          name: 'logs-endpoint.metadata_current-template@custom',
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Index template composed of the two component templates created
+    // with index pattern matching the destination index
+    expect(esClient.indices.putIndexTemplate.mock.calls).toEqual([
+      [
+        {
+          body: {
+            _meta: meta,
+            composed_of: [
+              'logs-endpoint.metadata_current-template@package',
+              'logs-endpoint.metadata_current-template@custom',
+            ],
+            index_patterns: ['.metrics-endpoint.metadata_united_default'],
+            priority: 250,
+            template: { mappings: undefined, settings: undefined },
+          },
+          name: 'logs-endpoint.metadata_current-template',
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Destination index is created before transform is created
+    expect(esClient.indices.create.mock.calls).toEqual([
+      [{ index: '.metrics-endpoint.metadata_united_default' }, { ignore: [400] }],
+    ]);
+
+    expect(esClient.transform.putTransform.mock.calls).toEqual([[expectedData.TRANSFORM]]);
+    expect(esClient.transform.startTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'logs-endpoint.metadata_current-default-0.16.0-dev.0',
+        },
+        { ignore: [409] },
+      ],
+    ]);
+
+    // Saved object is updated with newly created index templates, component templates, transform
+    expect(savedObjectsClient.update.mock.calls).toEqual([
+      [
+        'epm-packages',
+        'endpoint',
+        {
+          installed_es: [
+            {
+              id: 'metrics-endpoint.policy-0.16.0-dev.0',
+              type: ElasticsearchAssetType.ingestPipeline,
+            },
+            {
+              id: 'logs-endpoint.metadata_current-template',
+              type: ElasticsearchAssetType.indexTemplate,
+            },
+            {
+              id: 'logs-endpoint.metadata_current-template@custom',
+              type: ElasticsearchAssetType.componentTemplate,
+            },
+            {
+              id: 'logs-endpoint.metadata_current-template@package',
+              type: ElasticsearchAssetType.componentTemplate,
+            },
+            {
+              id: 'logs-endpoint.metadata_current-default-0.16.0-dev.0',
+              type: ElasticsearchAssetType.transform,
+            },
+          ],
+        },
+        {
+          refresh: false,
+        },
+      ],
+    ]);
+  });
+
+  test('can install new version when no older version', async () => {
+    const sourceData = getYamlTestData(true);
+    const expectedData = getExpectedData();
+
+    const previousInstallation: Installation = {
+      installed_es: [],
+    } as unknown as Installation;
+
+    const currentInstallation: Installation = {
+      installed_es: [
+        {
+          id: 'metrics-endpoint.metadata-current-default-0.16.0-dev.0',
+          type: ElasticsearchAssetType.transform,
+        },
+      ],
+    } as unknown as Installation;
+    (getAsset as jest.MockedFunction<typeof getAsset>).mockReturnValueOnce(
+      Buffer.from(sourceData.TRANSFORM, 'utf8')
+    );
+    (getInstallation as jest.MockedFunction<typeof getInstallation>)
+      .mockReturnValueOnce(Promise.resolve(previousInstallation))
+      .mockReturnValueOnce(Promise.resolve(currentInstallation));
+
+    (
+      getInstallationObject as jest.MockedFunction<typeof getInstallationObject>
+    ).mockReturnValueOnce(
+      Promise.resolve({
+        attributes: { installed_es: [] },
+      } as unknown as SavedObject<Installation>)
+    );
+
+    await installTransforms(
+      {
+        name: 'endpoint',
+        version: '0.16.0-dev.0',
+      } as unknown as RegistryPackage,
+      ['endpoint-0.16.0-dev.0/elasticsearch/transform/metadata_current/transform.yml'],
+      esClient,
+      savedObjectsClient,
+      loggerMock.create(),
+      previousInstallation.installed_es
+    );
+
+    expect(esClient.transform.putTransform.mock.calls).toEqual([[expectedData.TRANSFORM]]);
+    expect(esClient.transform.startTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'logs-endpoint.metadata_current-default-0.16.0-dev.0',
+        },
+        { ignore: [409] },
+      ],
+    ]);
+
+    expect(savedObjectsClient.update.mock.calls).toEqual([
+      [
+        'epm-packages',
+        'endpoint',
+        {
+          installed_es: [
+            { id: 'logs-endpoint.metadata_current-default-0.16.0-dev.0', type: 'transform' },
+          ],
+        },
+        {
+          refresh: false,
+        },
+      ],
+    ]);
+  });
+
+  test('can combine settings fields.yml & manifest.yml and not start transform automatically', async () => {
+    const sourceData = getYamlTestData(false);
+    const expectedData = getExpectedData();
+
+    const previousInstallation: Installation = {
+      installed_es: [
+        {
+          id: 'endpoint.metadata-current-default-0.15.0-dev.0',
+          type: ElasticsearchAssetType.transform,
+        },
+        {
+          id: 'logs-endpoint.metadata_current-template',
+          type: ElasticsearchAssetType.indexTemplate,
+        },
+        {
+          id: 'logs-endpoint.metadata_current-template@custom',
+          type: ElasticsearchAssetType.componentTemplate,
+        },
+        {
+          id: 'logs-endpoint.metadata_current-template@package',
+          type: ElasticsearchAssetType.componentTemplate,
+        },
+      ],
+    } as unknown as Installation;
+
+    const currentInstallation: Installation = {
+      installed_es: [],
+    } as unknown as Installation;
+
+    (getAsset as jest.MockedFunction<typeof getAsset>)
+      .mockReturnValueOnce(Buffer.from(sourceData.FIELDS, 'utf8'))
+      .mockReturnValueOnce(Buffer.from(sourceData.MANIFEST, 'utf8'))
+      .mockReturnValueOnce(Buffer.from(sourceData.TRANSFORM, 'utf8'));
+
+    (getInstallation as jest.MockedFunction<typeof getInstallation>)
+      .mockReturnValueOnce(Promise.resolve(previousInstallation))
+      .mockReturnValueOnce(Promise.resolve(currentInstallation));
+
+    (
+      getInstallationObject as jest.MockedFunction<typeof getInstallationObject>
+    ).mockReturnValueOnce(
+      Promise.resolve({
+        attributes: { installed_es: currentInstallation.installed_es },
+      } as unknown as SavedObject<Installation>)
+    );
+
+    esClient.transform.getTransform.mockResponseOnce({
+      count: 1,
+      transforms: [
+        // @ts-expect-error incomplete data
+        {
+          dest: {
+            index: 'mock-old-destination-index',
+          },
+        },
+      ],
+    });
+
+    await installTransforms(
+      {
+        name: 'endpoint',
+        version: '0.16.0-dev.0',
+      } as unknown as RegistryPackage,
+      [
+        'endpoint-0.16.0-dev.0/elasticsearch/transform/metadata_current/fields/fields.yml',
+        'endpoint-0.16.0-dev.0/elasticsearch/transform/metadata_current/manifest.yml',
+        'endpoint-0.16.0-dev.0/elasticsearch/transform/metadata_current/transform.yml',
+      ],
+      esClient,
+      savedObjectsClient,
+      loggerMock.create(),
+      previousInstallation.installed_es
+    );
+
+    expect(esClient.transform.getTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'endpoint.metadata-current-default-0.15.0-dev.0',
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Transform from old version is stopped & deleted
+    expect(esClient.transform.stopTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'endpoint.metadata-current-default-0.15.0-dev.0',
+          force: true,
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    expect(esClient.transform.deleteTransform.mock.calls).toEqual([
+      [
+        {
+          transform_id: 'endpoint.metadata-current-default-0.15.0-dev.0',
+          force: true,
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Destination index from old version is also deleted
+    expect(esClient.transport.request.mock.calls).toEqual([
+      [{ method: 'DELETE', path: '/mock-old-destination-index' }, { ignore: [404] }],
+    ]);
+
+    // Component templates are created with mappings from fields.yml
+    // and template from manifest
+    expect(esClient.cluster.putComponentTemplate.mock.calls).toEqual([
+      [
+        {
+          name: 'logs-endpoint.metadata_current-template@package',
+          body: {
+            template: {
+              settings: {
+                index: {
+                  codec: 'best_compression',
+                  refresh_interval: '5s',
+                  number_of_shards: 1,
+                  number_of_routing_shards: 30,
+                  hidden: true,
+                  mapping: { total_fields: { limit: '10000' } },
+                },
+              },
+              mappings: {
+                properties: { '@timestamp': { type: 'date' } },
+                dynamic_templates: [
+                  {
+                    strings_as_keyword: {
+                      match_mapping_type: 'string',
+                      mapping: { ignore_above: 1024, type: 'keyword' },
+                    },
+                  },
+                ],
+                dynamic: false,
+                _meta: {},
+                date_detection: false,
+              },
+            },
+            _meta: meta,
+          },
+          create: false,
+        },
+        { ignore: [404] },
+      ],
+      [
+        {
+          name: 'logs-endpoint.metadata_current-template@custom',
+          body: {
+            template: { settings: {} },
+            _meta: meta,
+          },
+          create: true,
+        },
+        { ignore: [404] },
+      ],
+    ]);
+    // Index template composed of the two component templates created
+    // with index pattern matching the destination index
+    expect(esClient.indices.putIndexTemplate.mock.calls).toEqual([
+      [
+        {
+          body: {
+            _meta: meta,
+            composed_of: [
+              'logs-endpoint.metadata_current-template@package',
+              'logs-endpoint.metadata_current-template@custom',
+            ],
+            index_patterns: ['.metrics-endpoint.metadata_united_default'],
+            priority: 250,
+            template: { mappings: undefined, settings: undefined },
+          },
+          name: 'logs-endpoint.metadata_current-template',
+        },
+        { ignore: [404] },
+      ],
+    ]);
+
+    // Destination index is created before transform is created
+    expect(esClient.indices.create.mock.calls).toEqual([
+      [{ index: '.metrics-endpoint.metadata_united_default' }, { ignore: [400] }],
+    ]);
+
+    // New transform created but not not started automatically if start: false in manifest.yml
+    expect(esClient.transform.putTransform.mock.calls).toEqual([[expectedData.TRANSFORM]]);
+    expect(esClient.transform.startTransform.mock.calls).toEqual([]);
+  });
+});