diff --git a/src/platform/plugins/private/links/common/index.ts b/src/platform/plugins/private/links/common/index.ts
index 92a4de7696241..550018cb63fac 100644
--- a/src/platform/plugins/private/links/common/index.ts
+++ b/src/platform/plugins/private/links/common/index.ts
@@ -8,3 +8,4 @@
  */
 
 export { APP_ICON, APP_NAME, CONTENT_ID, DISPLAY_NAME, LATEST_VERSION } from './constants';
+export { extractReferences, injectReferences } from './persistable_state';
diff --git a/src/platform/plugins/private/links/common/persistable_state/references.ts b/src/platform/plugins/private/links/common/persistable_state/references.ts
index 44f47f6f4dd3f..53f7966ccdb2a 100644
--- a/src/platform/plugins/private/links/common/persistable_state/references.ts
+++ b/src/platform/plugins/private/links/common/persistable_state/references.ts
@@ -67,18 +67,19 @@ export function injectReferences({
   }
 
   const { links } = attributes;
-  links.forEach((link) => {
+  const newLinks = links.map((link) => {
     if (link.type === DASHBOARD_LINK_TYPE && link.destinationRefName) {
       const reference = findReference(link.destinationRefName, references);
-      link.destination = reference.id;
-      delete link.destinationRefName;
+      const { destinationRefName, ...rest } = link;
+      return { ...rest, destination: reference.id };
     }
+    return link;
   });
 
   return {
     attributes: {
       ...attributes,
-      links,
+      links: newLinks,
     },
   };
 }
diff --git a/src/platform/plugins/private/links/common/types.ts b/src/platform/plugins/private/links/common/types.ts
index 922d6c5ae8ca4..fea7450836d26 100644
--- a/src/platform/plugins/private/links/common/types.ts
+++ b/src/platform/plugins/private/links/common/types.ts
@@ -8,7 +8,10 @@
  */
 
 import type { SavedObjectsResolveResponse } from '@kbn/core-saved-objects-api-server';
+import type { SerializedTitles } from '@kbn/presentation-publishing';
+import type { DynamicActionsSerializedState } from '@kbn/embeddable-enhanced-plugin/public/plugin';
 import { CONTENT_ID } from './constants';
+import { LinksAttributes } from './content_management';
 
 export type LinksContentType = typeof CONTENT_ID;
 
@@ -18,3 +21,15 @@ export interface SharingSavedObjectProps {
   aliasPurpose?: SavedObjectsResolveResponse['alias_purpose'];
   sourceId?: string;
 }
+
+export interface LinksByReferenceSerializedState {
+  savedObjectId: string;
+}
+
+export interface LinksByValueSerializedState {
+  attributes: LinksAttributes;
+}
+
+export type LinksSerializedState = SerializedTitles &
+  Partial<DynamicActionsSerializedState> &
+  (LinksByReferenceSerializedState | LinksByValueSerializedState);
diff --git a/src/platform/plugins/private/links/public/embeddable/links_embeddable.tsx b/src/platform/plugins/private/links/public/embeddable/links_embeddable.tsx
index 43d50920fb9a0..e9c1deeb1c249 100644
--- a/src/platform/plugins/private/links/public/embeddable/links_embeddable.tsx
+++ b/src/platform/plugins/private/links/public/embeddable/links_embeddable.tsx
@@ -8,7 +8,6 @@
  */
 
 import React, { createContext, useMemo } from 'react';
-import { cloneDeep } from 'lodash';
 import { BehaviorSubject } from 'rxjs';
 import { EuiListGroup, EuiPanel } from '@elastic/eui';
 
@@ -29,17 +28,13 @@ import {
 } from '../../common/content_management';
 import { DashboardLinkComponent } from '../components/dashboard_link/dashboard_link_component';
 import { ExternalLinkComponent } from '../components/external_link/external_link_component';
+import { LinksApi, LinksParentApi, LinksRuntimeState, ResolvedLink } from '../types';
+import { DISPLAY_NAME } from '../../common';
 import {
-  LinksApi,
   LinksByReferenceSerializedState,
   LinksByValueSerializedState,
-  LinksParentApi,
-  LinksRuntimeState,
   LinksSerializedState,
-  ResolvedLink,
-} from '../types';
-import { DISPLAY_NAME } from '../../common';
-import { injectReferences } from '../../common/persistable_state';
+} from '../../common/types';
 
 import '../components/links_component.scss';
 import { checkForDuplicateTitle, linksClient } from '../content_management';
@@ -61,8 +56,7 @@ export const getLinksEmbeddableFactory = () => {
   > = {
     type: CONTENT_ID,
     deserializeState: async (serializedState) => {
-      // Clone the state to avoid an object not extensible error when injecting references
-      const state = cloneDeep(serializedState.rawState);
+      const state = serializedState.rawState;
       const { title, description, hidePanelTitles } = serializedState.rawState;
 
       if (linksSerializeStateIsByReference(state)) {
@@ -76,21 +70,16 @@ export const getLinksEmbeddableFactory = () => {
         };
       }
 
-      const { attributes: attributesWithInjectedIds } = injectReferences({
-        attributes: state.attributes,
-        references: serializedState.references ?? [],
-      });
-
-      const resolvedLinks = await resolveLinks(attributesWithInjectedIds.links ?? []);
+      const resolvedLinks = await resolveLinks(state.attributes.links ?? []);
 
       return {
         title,
         description,
         hidePanelTitles,
         links: resolvedLinks,
-        layout: attributesWithInjectedIds.layout,
-        defaultPanelTitle: attributesWithInjectedIds.title,
-        defaultPanelDescription: attributesWithInjectedIds.description,
+        layout: state.attributes.layout,
+        defaultPanelTitle: state.attributes.title,
+        defaultPanelDescription: state.attributes.description,
       };
     },
     buildEmbeddable: async (state, buildApi, uuid, parentApi) => {
diff --git a/src/platform/plugins/private/links/public/lib/deserialize_from_library.ts b/src/platform/plugins/private/links/public/lib/deserialize_from_library.ts
index 725227d3a9f74..e08ecabd9f7e4 100644
--- a/src/platform/plugins/private/links/public/lib/deserialize_from_library.ts
+++ b/src/platform/plugins/private/links/public/lib/deserialize_from_library.ts
@@ -10,8 +10,9 @@
 import type { SOWithMetadata } from '@kbn/content-management-utils';
 import { LinksAttributes } from '../../common/content_management';
 import { injectReferences } from '../../common/persistable_state';
-import { LinksByReferenceSerializedState, LinksRuntimeState, LinksSerializedState } from '../types';
+import { LinksRuntimeState } from '../types';
 import { resolveLinks } from './resolve_links';
+import { LinksByReferenceSerializedState, LinksSerializedState } from '../../common/types';
 
 export const linksSerializeStateIsByReference = (
   state?: LinksSerializedState
diff --git a/src/platform/plugins/private/links/public/types.ts b/src/platform/plugins/private/links/public/types.ts
index aaa5e34faa236..17225af95ba56 100644
--- a/src/platform/plugins/private/links/public/types.ts
+++ b/src/platform/plugins/private/links/public/types.ts
@@ -18,14 +18,14 @@ import {
   SerializedTitles,
 } from '@kbn/presentation-publishing';
 import { DefaultEmbeddableApi } from '@kbn/embeddable-plugin/public';
-import { DynamicActionsSerializedState } from '@kbn/embeddable-enhanced-plugin/public/plugin';
 import { HasSerializedChildState, PresentationContainer } from '@kbn/presentation-containers';
 import { LocatorPublic } from '@kbn/share-plugin/common';
 import { DashboardLocatorParams, DASHBOARD_API_TYPE } from '@kbn/dashboard-plugin/public';
 import type { DashboardAttributes } from '@kbn/dashboard-plugin/server';
 
 import { CONTENT_ID } from '../common';
-import { Link, LinksAttributes, LinksLayoutType } from '../common/content_management';
+import { Link, LinksLayoutType } from '../common/content_management';
+import { LinksByReferenceSerializedState, LinksSerializedState } from '../common/types';
 
 export type LinksParentApi = PresentationContainer &
   HasType<typeof DASHBOARD_API_TYPE> &
@@ -42,18 +42,6 @@ export type LinksApi = HasType<typeof CONTENT_ID> &
   HasEditCapabilities &
   HasLibraryTransforms<LinksByReferenceSerializedState, LinksByValueSerializedState>;
 
-export interface LinksByReferenceSerializedState {
-  savedObjectId: string;
-}
-
-export interface LinksByValueSerializedState {
-  attributes: LinksAttributes;
-}
-
-export type LinksSerializedState = SerializedTitles &
-  Partial<DynamicActionsSerializedState> &
-  (LinksByReferenceSerializedState | LinksByValueSerializedState);
-
 export interface LinksRuntimeState
   extends Partial<LinksByReferenceSerializedState>,
     SerializedTitles {
diff --git a/src/platform/plugins/private/links/server/plugin.ts b/src/platform/plugins/private/links/server/plugin.ts
index c2d374f8d1e3c..20d71a0568b15 100644
--- a/src/platform/plugins/private/links/server/plugin.ts
+++ b/src/platform/plugins/private/links/server/plugin.ts
@@ -8,11 +8,15 @@
  */
 
 import { CoreSetup, CoreStart, Logger, Plugin, PluginInitializerContext } from '@kbn/core/server';
+import type { EmbeddableSetup } from '@kbn/embeddable-plugin/server';
 import type { ContentManagementServerSetup } from '@kbn/content-management-plugin/server';
-import { CONTENT_ID, LATEST_VERSION } from '../common';
+import { EmbeddableStateWithType } from '@kbn/embeddable-plugin/common';
+import { CONTENT_ID, LATEST_VERSION, extractReferences, injectReferences } from '../common';
 import { LinksAttributes } from '../common/content_management';
 import { LinksStorage } from './content_management';
 import { linksSavedObjectType } from './saved_objects';
+import { LinksSerializedState } from '../common/types';
+import { LinksByValueSerializedState } from '../common/types';
 
 export class LinksServerPlugin implements Plugin<object, object> {
   private readonly logger: Logger;
@@ -25,6 +29,7 @@ export class LinksServerPlugin implements Plugin<object, object> {
     core: CoreSetup,
     plugins: {
       contentManagement: ContentManagementServerSetup;
+      embeddable: EmbeddableSetup;
     }
   ) {
     plugins.contentManagement.register({
@@ -38,6 +43,39 @@ export class LinksServerPlugin implements Plugin<object, object> {
       },
     });
 
+    plugins.embeddable.registerEmbeddableFactory({
+      id: CONTENT_ID,
+      extract: (state) => {
+        const typedState = state as EmbeddableStateWithType & LinksSerializedState;
+        if (!('attributes' in typedState) || typedState.attributes === undefined) {
+          return { state, references: [] };
+        }
+
+        const { attributes, references } = extractReferences({
+          attributes: typedState.attributes,
+        } as LinksByValueSerializedState);
+        return {
+          state: { ...state, attributes },
+          references,
+        };
+      },
+      inject: (state, references) => {
+        const typedState = state as EmbeddableStateWithType & LinksSerializedState;
+        if (!('attributes' in typedState) || typedState.attributes === undefined) {
+          return typedState;
+        }
+
+        const { attributes } = injectReferences({
+          attributes: typedState.attributes,
+          references,
+        });
+        return {
+          ...typedState,
+          attributes,
+        };
+      },
+    });
+
     core.savedObjects.registerType<LinksAttributes>(linksSavedObjectType);
 
     return {};
diff --git a/src/platform/plugins/shared/controls/common/constants.ts b/src/platform/plugins/shared/controls/common/constants.ts
index d1f88567a3c6e..096ba4c3c4573 100644
--- a/src/platform/plugins/shared/controls/common/constants.ts
+++ b/src/platform/plugins/shared/controls/common/constants.ts
@@ -27,6 +27,7 @@ export const DEFAULT_IGNORE_PARENT_SETTINGS = {
 } as const;
 export const DEFAULT_AUTO_APPLY_SELECTIONS = true;
 
+export const REFERENCE_NAME_PREFIX = 'controlGroup_';
 export const TIME_SLIDER_CONTROL = 'timeSlider';
 export const RANGE_SLIDER_CONTROL = 'rangeSliderControl';
 export const OPTIONS_LIST_CONTROL = 'optionsListControl';
diff --git a/src/platform/plugins/shared/controls/common/index.ts b/src/platform/plugins/shared/controls/common/index.ts
index 1fd51fd92be9b..386072f52b7a5 100644
--- a/src/platform/plugins/shared/controls/common/index.ts
+++ b/src/platform/plugins/shared/controls/common/index.ts
@@ -26,6 +26,7 @@ export {
   CONTROL_WIDTH_OPTIONS,
   CONTROL_CHAINING_OPTIONS,
   CONTROL_LABEL_POSITION_OPTIONS,
+  REFERENCE_NAME_PREFIX,
   OPTIONS_LIST_CONTROL,
   RANGE_SLIDER_CONTROL,
   TIME_SLIDER_CONTROL,
diff --git a/src/platform/plugins/shared/controls/public/controls/data_controls/reference_name_utils.ts b/src/platform/plugins/shared/controls/public/controls/data_controls/reference_name_utils.ts
index 43dc37610f66c..f1323975e81ba 100644
--- a/src/platform/plugins/shared/controls/public/controls/data_controls/reference_name_utils.ts
+++ b/src/platform/plugins/shared/controls/public/controls/data_controls/reference_name_utils.ts
@@ -7,7 +7,7 @@
  * License v3.0 only", or the "Server Side Public License, v 1".
  */
 
-const REFERENCE_NAME_PREFIX = 'controlGroup_';
+import { REFERENCE_NAME_PREFIX } from '../../../common';
 
 export function getReferenceName(controlId: string, referenceNameSuffix: string) {
   return `${REFERENCE_NAME_PREFIX}${controlId}:${referenceNameSuffix}`;
diff --git a/src/platform/plugins/shared/dashboard/common/dashboard_container/persistable_state/dashboard_container_references.ts b/src/platform/plugins/shared/dashboard/common/dashboard_container/persistable_state/dashboard_container_references.ts
index 0a331c8c253fd..94110f307d4d3 100644
--- a/src/platform/plugins/shared/dashboard/common/dashboard_container/persistable_state/dashboard_container_references.ts
+++ b/src/platform/plugins/shared/dashboard/common/dashboard_container/persistable_state/dashboard_container_references.ts
@@ -13,6 +13,7 @@ import {
   EmbeddablePersistableStateService,
   EmbeddableStateWithType,
 } from '@kbn/embeddable-plugin/common';
+import { REFERENCE_NAME_PREFIX } from '@kbn/controls-plugin/common';
 import { ParsedDashboardAttributesWithType } from '../../types';
 
 export const getReferencesForPanelId = (id: string, references: Reference[]): Reference[] => {
@@ -24,7 +25,7 @@ export const getReferencesForPanelId = (id: string, references: Reference[]): Re
 };
 
 export const getReferencesForControls = (references: Reference[]): Reference[] => {
-  return references.filter((reference) => reference.name.startsWith(controlGroupReferencePrefix));
+  return references.filter((reference) => reference.name.startsWith(REFERENCE_NAME_PREFIX));
 };
 
 export const prefixReferencesFromPanel = (id: string, references: Reference[]): Reference[] => {
@@ -37,8 +38,6 @@ export const prefixReferencesFromPanel = (id: string, references: Reference[]):
     }));
 };
 
-const controlGroupReferencePrefix = 'controlGroup_';
-
 export const createInject = (
   persistableStateService: EmbeddablePersistableStateService
 ): EmbeddablePersistableStateService['inject'] => {
diff --git a/src/platform/plugins/shared/dashboard/common/index.ts b/src/platform/plugins/shared/dashboard/common/index.ts
index c8c988d5c461e..137f29e6a3a07 100644
--- a/src/platform/plugins/shared/dashboard/common/index.ts
+++ b/src/platform/plugins/shared/dashboard/common/index.ts
@@ -27,7 +27,11 @@ export {
   createExtract,
 } from './dashboard_container/persistable_state/dashboard_container_references';
 
-export { prefixReferencesFromPanel } from './dashboard_container/persistable_state/dashboard_container_references';
+export {
+  prefixReferencesFromPanel,
+  getReferencesForControls,
+  getReferencesForPanelId,
+} from './dashboard_container/persistable_state/dashboard_container_references';
 
 export {
   convertPanelsArrayToPanelMap,
diff --git a/src/platform/plugins/shared/dashboard/server/content_management/dashboard_storage.ts b/src/platform/plugins/shared/dashboard/server/content_management/dashboard_storage.ts
index d113d509f5e89..8338c893be9c8 100644
--- a/src/platform/plugins/shared/dashboard/server/content_management/dashboard_storage.ts
+++ b/src/platform/plugins/shared/dashboard/server/content_management/dashboard_storage.ts
@@ -17,10 +17,11 @@ import type { Logger } from '@kbn/logging';
 
 import { CreateResult, DeleteResult, SearchQuery } from '@kbn/content-management-plugin/common';
 import { StorageContext } from '@kbn/content-management-plugin/server';
+import { EmbeddableStart } from '@kbn/embeddable-plugin/server';
 import { DASHBOARD_SAVED_OBJECT_TYPE } from '../dashboard_saved_object';
 import { cmServicesDefinition } from './cm_services';
 import { DashboardSavedObjectAttributes } from '../dashboard_saved_object';
-import { itemAttrsToSavedObjectAttrs, savedObjectToItem } from './latest';
+import { itemAttrsToSavedObject, savedObjectToItem } from './latest';
 import type {
   DashboardAttributes,
   DashboardItem,
@@ -62,10 +63,13 @@ export class DashboardStorage {
   constructor({
     logger,
     throwOnResultValidationError,
+    embeddable,
   }: {
     logger: Logger;
     throwOnResultValidationError: boolean;
+    embeddable: EmbeddableStart;
   }) {
+    this.embeddable = embeddable;
     this.logger = logger;
     this.throwOnResultValidationError = throwOnResultValidationError ?? false;
     this.mSearch = {
@@ -76,6 +80,7 @@ export class DashboardStorage {
 
         const { item, error: itemError } = savedObjectToItem(
           savedObject as SavedObjectsFindResult<DashboardSavedObjectAttributes>,
+          this.embeddable,
           false
         );
         if (itemError) {
@@ -110,6 +115,7 @@ export class DashboardStorage {
     };
   }
 
+  private embeddable: EmbeddableStart;
   private logger: Logger;
   private throwOnResultValidationError: boolean;
 
@@ -131,7 +137,7 @@ export class DashboardStorage {
       outcome,
     } = await soClient.resolve<DashboardSavedObjectAttributes>(DASHBOARD_SAVED_OBJECT_TYPE, id);
 
-    const { item, error: itemError } = savedObjectToItem(savedObject, false);
+    const { item, error: itemError } = savedObjectToItem(savedObject, this.embeddable, false);
     if (itemError) {
       throw Boom.badRequest(`Invalid response. ${itemError.message}`);
     }
@@ -194,8 +200,11 @@ export class DashboardStorage {
       throw Boom.badRequest(`Invalid options. ${optionsError.message}`);
     }
 
-    const { attributes: soAttributes, error: attributesError } =
-      itemAttrsToSavedObjectAttrs(dataToLatest);
+    const {
+      attributes: soAttributes,
+      references: soReferences,
+      error: attributesError,
+    } = itemAttrsToSavedObject(dataToLatest, this.embeddable, options.references);
     if (attributesError) {
       throw Boom.badRequest(`Invalid data. ${attributesError.message}`);
     }
@@ -204,10 +213,10 @@ export class DashboardStorage {
     const savedObject = await soClient.create<DashboardSavedObjectAttributes>(
       DASHBOARD_SAVED_OBJECT_TYPE,
       soAttributes,
-      optionsToLatest
+      { ...optionsToLatest, references: soReferences }
     );
 
-    const { item, error: itemError } = savedObjectToItem(savedObject, false);
+    const { item, error: itemError } = savedObjectToItem(savedObject, this.embeddable, false);
     if (itemError) {
       throw Boom.badRequest(`Invalid response. ${itemError.message}`);
     }
@@ -263,8 +272,11 @@ export class DashboardStorage {
       throw Boom.badRequest(`Invalid options. ${optionsError.message}`);
     }
 
-    const { attributes: soAttributes, error: attributesError } =
-      itemAttrsToSavedObjectAttrs(dataToLatest);
+    const {
+      attributes: soAttributes,
+      references: soReferences,
+      error: attributesError,
+    } = itemAttrsToSavedObject(dataToLatest, this.embeddable, options.references);
     if (attributesError) {
       throw Boom.badRequest(`Invalid data. ${attributesError.message}`);
     }
@@ -274,10 +286,10 @@ export class DashboardStorage {
       DASHBOARD_SAVED_OBJECT_TYPE,
       id,
       soAttributes,
-      optionsToLatest
+      { ...optionsToLatest, references: soReferences }
     );
 
-    const { item, error: itemError } = savedObjectToItem(partialSavedObject, true);
+    const { item, error: itemError } = savedObjectToItem(partialSavedObject, this.embeddable, true);
     if (itemError) {
       throw Boom.badRequest(`Invalid response. ${itemError.message}`);
     }
@@ -341,7 +353,7 @@ export class DashboardStorage {
     const soResponse = await soClient.find<DashboardSavedObjectAttributes>(soQuery);
     const hits = soResponse.saved_objects
       .map((so) => {
-        const { item } = savedObjectToItem(so, false, {
+        const { item } = savedObjectToItem(so, this.embeddable, false, {
           allowedAttributes: soQuery.fields,
           allowedReferences: optionsToLatest?.includeReferences,
         });
diff --git a/src/platform/plugins/shared/dashboard/server/content_management/v3/index.ts b/src/platform/plugins/shared/dashboard/server/content_management/v3/index.ts
index 7be9313c3210e..32a5469fcf72c 100644
--- a/src/platform/plugins/shared/dashboard/server/content_management/v3/index.ts
+++ b/src/platform/plugins/shared/dashboard/server/content_management/v3/index.ts
@@ -37,6 +37,6 @@ export {
 } from './cm_services';
 export {
   dashboardAttributesOut,
-  itemAttrsToSavedObjectAttrs,
+  itemAttrsToSavedObject,
   savedObjectToItem,
 } from './transform_utils';
diff --git a/src/platform/plugins/shared/dashboard/server/content_management/v3/transform_utils.ts b/src/platform/plugins/shared/dashboard/server/content_management/v3/transform_utils.ts
index 18c9085df4ec0..48676b36125da 100644
--- a/src/platform/plugins/shared/dashboard/server/content_management/v3/transform_utils.ts
+++ b/src/platform/plugins/shared/dashboard/server/content_management/v3/transform_utils.ts
@@ -25,14 +25,16 @@ import {
 } from '@kbn/controls-plugin/common';
 import { SerializedSearchSourceFields, parseSearchSourceJSON } from '@kbn/data-plugin/common';
 
+import { EmbeddableStart } from '@kbn/embeddable-plugin/server';
 import type { SavedObject, SavedObjectReference } from '@kbn/core-saved-objects-api-server';
+import { getReferencesForPanelId, prefixReferencesFromPanel } from '../../../common';
 import type {
   ControlGroupAttributes,
   DashboardAttributes,
   DashboardGetOut,
   DashboardItem,
   DashboardOptions,
-  ItemAttrsToSavedObjectAttrsReturn,
+  ItemAttrsToSavedObjectReturn,
   PartialDashboardItem,
   SavedObjectToItemReturn,
 } from './types';
@@ -131,24 +133,37 @@ function optionsOut(optionsJSON: string): DashboardAttributes['options'] {
   };
 }
 
-function panelsOut(panelsJSON: string): DashboardAttributes['panels'] {
+function panelsOut(
+  panelsJSON: string,
+  references: SavedObjectReference[],
+  embeddable: EmbeddableStart
+): DashboardAttributes['panels'] {
   const panels = JSON.parse(panelsJSON) as SavedDashboardPanel[];
   return panels.map(
-    ({ embeddableConfig, gridData, id, panelIndex, panelRefName, title, type, version }) => ({
-      gridData,
-      id,
-      panelConfig: embeddableConfig,
-      panelIndex,
-      panelRefName,
-      title,
-      type,
-      version,
-    })
+    ({ embeddableConfig, gridData, id, panelIndex, panelRefName, title, type, version }) => {
+      const panelReferences = getReferencesForPanelId(panelIndex, references);
+      const { type: embeddableType, ...injectedAttributes } = embeddable.inject(
+        { type, ...embeddableConfig },
+        panelReferences
+      );
+      return {
+        gridData,
+        id,
+        panelConfig: injectedAttributes,
+        panelIndex,
+        panelRefName,
+        title,
+        type,
+        version,
+      };
+    }
   );
 }
 
 export function dashboardAttributesOut(
-  attributes: DashboardSavedObjectAttributes | Partial<DashboardSavedObjectAttributes>
+  attributes: DashboardSavedObjectAttributes | Partial<DashboardSavedObjectAttributes>,
+  references: SavedObjectReference[],
+  embeddable: EmbeddableStart
 ): DashboardAttributes | Partial<DashboardAttributes> {
   const {
     controlGroupInput,
@@ -171,7 +186,7 @@ export function dashboardAttributesOut(
       kibanaSavedObjectMeta: kibanaSavedObjectMetaOut(kibanaSavedObjectMeta),
     }),
     ...(optionsJSON && { options: optionsOut(optionsJSON) }),
-    ...(panelsJSON && { panels: panelsOut(panelsJSON) }),
+    ...(panelsJSON && { panels: panelsOut(panelsJSON, references, embeddable) }),
     ...(refreshInterval && {
       refreshInterval: { pause: refreshInterval.pause, value: refreshInterval.value },
     }),
@@ -206,13 +221,31 @@ function controlGroupInputIn(
 }
 
 function panelsIn(
-  panels: DashboardAttributes['panels']
+  panels: DashboardAttributes['panels'],
+  embeddable: EmbeddableStart,
+  references: SavedObjectReference[],
+  incomingReferences?: SavedObjectReference[]
 ): DashboardSavedObjectAttributes['panelsJSON'] {
-  const updatedPanels = panels.map(({ panelIndex, gridData, panelConfig, ...restPanel }) => {
+  const updatedPanels = panels.map(({ panelIndex, gridData, type, panelConfig, ...restPanel }) => {
     const idx = panelIndex ?? uuidv4();
+    const updatedPanelConfig = incomingReferences
+      ? embeddable.inject(
+          {
+            type,
+            ...panelConfig,
+          },
+          getReferencesForPanelId(idx, incomingReferences)
+        )
+      : panelConfig;
+    const { state: extractedPanelConfig, references: panelReferences } = embeddable.extract({
+      type,
+      ...updatedPanelConfig,
+    });
+    references.push(...prefixReferencesFromPanel(idx, panelReferences));
     return {
       ...restPanel,
-      embeddableConfig: panelConfig,
+      type,
+      embeddableConfig: extractedPanelConfig,
       panelIndex: idx,
       gridData: {
         ...gridData,
@@ -274,9 +307,12 @@ export const getResultV3ToV2 = (result: DashboardGetOut): DashboardCrudTypesV2['
   };
 };
 
-export const itemAttrsToSavedObjectAttrs = (
-  attributes: DashboardAttributes
-): ItemAttrsToSavedObjectAttrsReturn => {
+export const itemAttrsToSavedObject = (
+  attributes: DashboardAttributes,
+  embeddable: EmbeddableStart,
+  incomingReferences?: SavedObjectReference[]
+): ItemAttrsToSavedObjectReturn => {
+  const soReferences: SavedObjectReference[] = [];
   try {
     const { controlGroupInput, kibanaSavedObjectMeta, options, panels, ...rest } = attributes;
     const soAttributes = {
@@ -288,15 +324,15 @@ export const itemAttrsToSavedObjectAttrs = (
         optionsJSON: JSON.stringify(options),
       }),
       ...(panels && {
-        panelsJSON: panelsIn(panels),
+        panelsJSON: panelsIn(panels, embeddable, soReferences, incomingReferences),
       }),
       ...(kibanaSavedObjectMeta && {
         kibanaSavedObjectMeta: kibanaSavedObjectMetaIn(kibanaSavedObjectMeta),
       }),
     };
-    return { attributes: soAttributes, error: null };
+    return { attributes: soAttributes, references: soReferences, error: null };
   } catch (e) {
-    return { attributes: null, error: e };
+    return { attributes: null, references: null, error: e };
   }
 };
 
@@ -317,12 +353,14 @@ export interface SavedObjectToItemOptions {
 
 export function savedObjectToItem(
   savedObject: SavedObject<DashboardSavedObjectAttributes>,
+  embeddable: EmbeddableStart,
   partial: false,
   opts?: SavedObjectToItemOptions
 ): SavedObjectToItemReturn<DashboardItem>;
 
 export function savedObjectToItem(
   savedObject: PartialSavedObject<DashboardSavedObjectAttributes>,
+  embeddable: EmbeddableStart,
   partial: true,
   opts?: SavedObjectToItemOptions
 ): SavedObjectToItemReturn<PartialDashboardItem>;
@@ -331,6 +369,7 @@ export function savedObjectToItem(
   savedObject:
     | SavedObject<DashboardSavedObjectAttributes>
     | PartialSavedObject<DashboardSavedObjectAttributes>,
+  embeddable: EmbeddableStart,
   partial: boolean /* partial arg is used to enforce the correct savedObject type */,
   { allowedAttributes, allowedReferences }: SavedObjectToItemOptions = {}
 ): SavedObjectToItemReturn<DashboardItem | PartialDashboardItem> {
@@ -344,15 +383,15 @@ export function savedObjectToItem(
     attributes,
     error,
     namespaces,
-    references,
+    references = [],
     version,
     managed,
   } = savedObject;
 
   try {
     const attributesOut = allowedAttributes
-      ? pick(dashboardAttributesOut(attributes), allowedAttributes)
-      : dashboardAttributesOut(attributes);
+      ? pick(dashboardAttributesOut(attributes, references, embeddable), allowedAttributes)
+      : dashboardAttributesOut(attributes, references, embeddable);
 
     // if includeReferences is provided, only include references of those types
     const referencesOut = allowedReferences
diff --git a/src/platform/plugins/shared/dashboard/server/content_management/v3/types.ts b/src/platform/plugins/shared/dashboard/server/content_management/v3/types.ts
index 0c7144569aba2..87ba378bcd296 100644
--- a/src/platform/plugins/shared/dashboard/server/content_management/v3/types.ts
+++ b/src/platform/plugins/shared/dashboard/server/content_management/v3/types.ts
@@ -81,12 +81,14 @@ export type SavedObjectToItemReturn<T> =
       error: Error;
     };
 
-export type ItemAttrsToSavedObjectAttrsReturn =
+export type ItemAttrsToSavedObjectReturn =
   | {
       attributes: DashboardSavedObjectAttributes;
+      references: SavedObjectReference[];
       error: null;
     }
   | {
       attributes: null;
+      references: null;
       error: Error;
     };
diff --git a/src/platform/plugins/shared/dashboard/server/plugin.ts b/src/platform/plugins/shared/dashboard/server/plugin.ts
index a102fb39eaf34..56c85ce021009 100644
--- a/src/platform/plugins/shared/dashboard/server/plugin.ts
+++ b/src/platform/plugins/shared/dashboard/server/plugin.ts
@@ -11,7 +11,7 @@ import {
   TaskManagerSetupContract,
   TaskManagerStartContract,
 } from '@kbn/task-manager-plugin/server';
-import { EmbeddableSetup } from '@kbn/embeddable-plugin/server';
+import { EmbeddableSetup, EmbeddableStart } from '@kbn/embeddable-plugin/server';
 import { UsageCollectionSetup, UsageCollectionStart } from '@kbn/usage-collection-plugin/server';
 import { ContentManagementServerSetup } from '@kbn/content-management-plugin/server';
 import { PluginInitializerContext, CoreSetup, CoreStart, Plugin, Logger } from '@kbn/core/server';
@@ -42,6 +42,7 @@ interface SetupDeps {
 interface StartDeps {
   taskManager: TaskManagerStartContract;
   usageCollection?: UsageCollectionStart;
+  embeddable: EmbeddableStart;
 }
 
 export class DashboardPlugin
@@ -69,6 +70,7 @@ export class DashboardPlugin
       storage: new DashboardStorage({
         throwOnResultValidationError: this.initializerContext.env.mode.dev,
         logger: this.logger.get('storage'),
+        embeddable: plugins.embeddable,
       }),
       version: {
         latest: LATEST_VERSION,