diff --git a/packages/data/src/plugins/persistence/index.js b/packages/data/src/plugins/persistence/index.js
index 0bf50f768269d..8a3eb27df01e7 100644
--- a/packages/data/src/plugins/persistence/index.js
+++ b/packages/data/src/plugins/persistence/index.js
@@ -1,7 +1,7 @@
 /**
  * External dependencies
  */
-import { merge, isPlainObject } from 'lodash';
+import { merge, isPlainObject, reduce } from 'lodash';
 
 /**
  * Internal dependencies
@@ -402,6 +402,122 @@ export function migrateThirdPartyFeaturePreferencesToPreferencesStore(
 	}
 }
 
+/**
+ * Migrates interface 'enableItems' data to the preferences store.
+ *
+ * The interface package stores this data in this format:
+ * ```js
+ * {
+ *     enableItems: {
+ *         singleEnableItems: {
+ * 	           complementaryArea: {
+ *                 'core/edit-post': 'edit-post/document',
+ *                 'core/edit-site': 'edit-site/global-styles',
+ *             }
+ *         },
+ *         multipleEnableItems: {
+ *             pinnedItems: {
+ *                 'core/edit-post': {
+ *                     'plugin-1': true,
+ *                 },
+ *                 'core/edit-site': {
+ *                     'plugin-2': true,
+ *                 },
+ *             },
+ *         }
+ *     }
+ * }
+ * ```
+ * and it should be migrated it to:
+ * ```js
+ * {
+ *     'core/edit-post': {
+ *         complementaryArea: 'edit-post/document',
+ *         pinnedItems: {
+ *             'plugin-1': true,
+ *         },
+ *     },
+ *     'core/edit-site': {
+ *         complementaryArea: 'edit-site/global-styles',
+ *         pinnedItems: {
+ *             'plugin-2': true,
+ *         },
+ *     },
+ * }
+ * ```
+ *
+ * @param {Object} persistence The persistence interface.
+ */
+export function migrateInterfaceEnableItemsToPreferencesStore( persistence ) {
+	const interfaceStoreName = 'core/interface';
+	const preferencesStoreName = 'core/preferences';
+	const state = persistence.get();
+	const sourceEnableItems = state[ interfaceStoreName ]?.enableItems;
+
+	// There's nothing to migrate, exit early.
+	if ( ! sourceEnableItems ) {
+		return;
+	}
+
+	const allPreferences = state[ preferencesStoreName ]?.preferences ?? {};
+
+	// First convert complementaryAreas into the right format.
+	// Use the existing preferences as the accumulator so that the data is
+	// merged.
+	const sourceComplementaryAreas =
+		sourceEnableItems?.singleEnableItems?.complementaryArea;
+	const convertedComplementaryAreas = reduce(
+		sourceComplementaryAreas,
+		( accumulator, data, scope ) => {
+			// Don't overwrite any existing data in the preferences store.
+			if ( accumulator[ scope ]?.complementaryArea ) {
+				return accumulator;
+			}
+
+			return {
+				...accumulator,
+				[ scope ]: {
+					...accumulator[ scope ],
+					complementaryArea: data,
+				},
+			};
+		},
+		allPreferences
+	);
+
+	// Next feed the converted complementary areas back into a reducer that
+	// converts the pinned items, resulting in the fully migrated data.
+	const sourcePinnedItems =
+		sourceEnableItems?.multipleEnableItems?.pinnedItems;
+	const allConvertedData = reduce(
+		sourcePinnedItems,
+		( accumulator, data, scope ) => {
+			// Don't overwrite any existing data in the preferences store.
+			if ( accumulator[ scope ]?.pinnedItems ) {
+				return accumulator;
+			}
+
+			return {
+				...accumulator,
+				[ scope ]: {
+					...accumulator[ scope ],
+					pinnedItems: data,
+				},
+			};
+		},
+		convertedComplementaryAreas
+	);
+
+	persistence.set( preferencesStoreName, {
+		preferences: allConvertedData,
+	} );
+
+	// Remove migrated preferences.
+	persistence.set( interfaceStoreName, {
+		enableItems: undefined,
+	} );
+}
+
 persistencePlugin.__unstableMigrate = ( pluginOptions ) => {
 	const persistence = createPersistenceInterface( pluginOptions );
 
@@ -445,6 +561,7 @@ persistencePlugin.__unstableMigrate = ( pluginOptions ) => {
 		'core/edit-site',
 		'editorMode'
 	);
+	migrateInterfaceEnableItemsToPreferencesStore( persistence );
 };
 
 export default persistencePlugin;
diff --git a/packages/data/src/plugins/persistence/test/index.js b/packages/data/src/plugins/persistence/test/index.js
index 704c9231615ae..ca327155b9712 100644
--- a/packages/data/src/plugins/persistence/test/index.js
+++ b/packages/data/src/plugins/persistence/test/index.js
@@ -12,6 +12,7 @@ import plugin, {
 	migrateFeaturePreferencesToPreferencesStore,
 	migrateThirdPartyFeaturePreferencesToPreferencesStore,
 	migrateIndividualPreferenceToPreferencesStore,
+	migrateInterfaceEnableItemsToPreferencesStore,
 } from '../';
 import objectStorage from '../storage/object';
 import { createRegistry } from '../../../';
@@ -923,3 +924,122 @@ describe( 'migrateThirdPartyFeaturePreferencesToPreferencesStore', () => {
 		} );
 	} );
 } );
+
+describe( 'migrateInterfaceEnableItemsToPreferencesStore', () => {
+	it( 'migrates enableItems to the preferences store', () => {
+		const persistenceInterface = createPersistenceInterface( {
+			storageKey: 'test-username',
+		} );
+
+		persistenceInterface.set( 'core/interface', {
+			enableItems: {
+				singleEnableItems: {
+					complementaryArea: {
+						'core/edit-post': 'edit-post/document',
+						'core/edit-site': 'edit-site/global-styles',
+					},
+				},
+				multipleEnableItems: {
+					pinnedItems: {
+						'core/edit-post': {
+							'plugin-1': true,
+						},
+						'core/edit-site': {
+							'plugin-2': true,
+						},
+					},
+				},
+			},
+		} );
+
+		migrateInterfaceEnableItemsToPreferencesStore( persistenceInterface );
+
+		expect( persistenceInterface.get() ).toEqual( {
+			'core/preferences': {
+				preferences: {
+					'core/edit-post': {
+						complementaryArea: 'edit-post/document',
+						pinnedItems: {
+							'plugin-1': true,
+						},
+					},
+					'core/edit-site': {
+						complementaryArea: 'edit-site/global-styles',
+						pinnedItems: {
+							'plugin-2': true,
+						},
+					},
+				},
+			},
+			'core/interface': {
+				enableItems: undefined,
+			},
+		} );
+	} );
+
+	it( 'merges pinnedItems and complementaryAreas with existing preferences store data', () => {
+		const persistenceInterface = createPersistenceInterface( {
+			storageKey: 'test-username',
+		} );
+
+		persistenceInterface.set( 'core/interface', {
+			enableItems: {
+				singleEnableItems: {
+					complementaryArea: {
+						'core/edit-post': 'edit-post/document',
+						'core/edit-site': 'edit-site/global-styles',
+					},
+				},
+				multipleEnableItems: {
+					pinnedItems: {
+						'core/edit-post': {
+							'plugin-1': true,
+						},
+						'core/edit-site': {
+							'plugin-2': true,
+						},
+					},
+				},
+			},
+		} );
+
+		persistenceInterface.set( 'core/preferences', {
+			preferences: {
+				'core/edit-post': {
+					preferenceA: 1,
+					preferenceB: 2,
+				},
+				'core/edit-site': {
+					preferenceC: true,
+				},
+			},
+		} );
+
+		migrateInterfaceEnableItemsToPreferencesStore( persistenceInterface );
+
+		expect( persistenceInterface.get() ).toEqual( {
+			'core/preferences': {
+				preferences: {
+					'core/edit-post': {
+						preferenceA: 1,
+						preferenceB: 2,
+						complementaryArea: 'edit-post/document',
+						pinnedItems: {
+							'plugin-1': true,
+						},
+					},
+					'core/edit-site': {
+						preferenceC: true,
+						complementaryArea: 'edit-site/global-styles',
+						pinnedItems: {
+							'plugin-2': true,
+						},
+					},
+				},
+			},
+			'core/interface': {
+				enableItems: undefined,
+			},
+		} );
+	} );
+} );