diff --git a/src/platform/plugins/shared/discover/common/embeddable/get_transform_in.ts b/src/platform/plugins/shared/discover/common/embeddable/get_transform_in.ts
index bac4daa26e39c..ff66dce2fd9b9 100644
--- a/src/platform/plugins/shared/discover/common/embeddable/get_transform_in.ts
+++ b/src/platform/plugins/shared/discover/common/embeddable/get_transform_in.ts
@@ -7,15 +7,16 @@
  * License v3.0 only", or the "Server Side Public License, v 1".
  */
 
+import { omit } from 'lodash';
 import { SavedSearchType } from '@kbn/saved-search-plugin/common';
 import type { SavedObjectReference } from '@kbn/core/server';
+import { extractReferences, parseSearchSourceJSON } from '@kbn/data-plugin/common';
 import type { DrilldownTransforms } from '@kbn/embeddable-plugin/common';
 import type {
   SearchEmbeddableByReferenceState,
   SearchEmbeddableState,
   StoredSearchEmbeddableState,
 } from './types';
-import { extract } from './search_inject_extract';
 
 export const SAVED_SEARCH_SAVED_OBJECT_REF_NAME = 'savedObjectRef';
 
@@ -47,22 +48,38 @@ export function getTransformIn(transformDrilldownsIn: DrilldownTransforms['trans
     }
 
     // by value
-    const { state: extractedState, references } = extract({
-      type: SavedSearchType,
-      attributes: storedState.attributes,
+    const tabReferences: SavedObjectReference[] = [];
+    const tabs = storedState.attributes.tabs.map((tab) => {
+      try {
+        const searchSourceValues = parseSearchSourceJSON(
+          tab.attributes.kibanaSavedObjectMeta.searchSourceJSON
+        );
+        const [searchSourceFields, searchSourceReferences] = extractReferences(searchSourceValues);
+        tabReferences.push(...searchSourceReferences);
+        return {
+          ...tab,
+          attributes: {
+            ...tab.attributes,
+            kibanaSavedObjectMeta: {
+              ...tab.attributes.kibanaSavedObjectMeta,
+              searchSourceJSON: JSON.stringify(searchSourceFields),
+            },
+          },
+        };
+      } catch (e) {
+        return tab;
+      }
     });
 
     return {
       state: {
         ...storedState,
         attributes: {
-          ...storedState.attributes,
-          ...extractedState.attributes,
-          // discover session stores references as part of attributes
-          references,
+          ...omit(storedState.attributes, 'references'),
+          tabs,
         },
       },
-      references: [...references, ...drilldownReferences],
+      references: [...tabReferences, ...drilldownReferences],
     };
   }
   return transformIn;
diff --git a/src/platform/plugins/shared/discover/common/embeddable/get_transform_out.ts b/src/platform/plugins/shared/discover/common/embeddable/get_transform_out.ts
index 932dea7c1aef0..96f94d5f94dc1 100644
--- a/src/platform/plugins/shared/discover/common/embeddable/get_transform_out.ts
+++ b/src/platform/plugins/shared/discover/common/embeddable/get_transform_out.ts
@@ -7,18 +7,18 @@
  * License v3.0 only", or the "Server Side Public License, v 1".
  */
 
+import { flow, omit } from 'lodash';
 import { extractTabs, SavedSearchType } from '@kbn/saved-search-plugin/common';
+import { injectReferences, parseSearchSourceJSON } from '@kbn/data-plugin/common';
 import type { DrilldownTransforms } from '@kbn/embeddable-plugin/common';
 import type { SavedObjectReference } from '@kbn/core/server';
 import { transformTitlesOut } from '@kbn/presentation-publishing';
-import { flow } from 'lodash';
 import type {
   SearchEmbeddableByReferenceState,
   SearchEmbeddableByValueState,
   StoredSearchEmbeddableByValueState,
   StoredSearchEmbeddableState,
 } from './types';
-import { inject } from './search_inject_extract';
 import { SAVED_SEARCH_SAVED_OBJECT_REF_NAME } from './get_transform_in';
 
 function isByValue(
@@ -42,14 +42,34 @@ export function getTransformOut(transformDrilldownsOut: DrilldownTransforms['tra
     const state = transformsFlow(storedState);
 
     if (isByValue(state)) {
-      const tabsState = {
-        ...state,
-        attributes: extractTabs(state.attributes),
-      };
-      const { attributes } = inject({ type: SavedSearchType, ...tabsState }, references ?? []);
+      const tabsState = { ...state, attributes: extractTabs(state.attributes) };
+      const tabs = tabsState.attributes.tabs.map((tab) => {
+        try {
+          const searchSourceValues = parseSearchSourceJSON(
+            tab.attributes.kibanaSavedObjectMeta.searchSourceJSON
+          );
+          const searchSourceFields = injectReferences(searchSourceValues, references ?? []);
+          return {
+            ...tab,
+            attributes: {
+              ...omit(tab.attributes, 'references'),
+              kibanaSavedObjectMeta: {
+                ...tab.attributes.kibanaSavedObjectMeta,
+                searchSourceJSON: JSON.stringify(searchSourceFields),
+              },
+            },
+          };
+        } catch (e) {
+          return tab;
+        }
+      });
+
       return {
         ...state,
-        attributes,
+        attributes: {
+          ...state.attributes,
+          tabs,
+        },
       } as SearchEmbeddableByValueState;
     }
 
diff --git a/src/platform/plugins/shared/discover/common/embeddable/index.ts b/src/platform/plugins/shared/discover/common/embeddable/index.ts
index 9e2055fcf02b9..b383982938a5c 100644
--- a/src/platform/plugins/shared/discover/common/embeddable/index.ts
+++ b/src/platform/plugins/shared/discover/common/embeddable/index.ts
@@ -7,5 +7,4 @@
  * License v3.0 only", or the "Server Side Public License, v 1".
  */
 
-export { inject, extract } from './search_inject_extract';
 export { getSearchEmbeddableTransforms } from './search_embeddable_transforms';
diff --git a/src/platform/plugins/shared/discover/common/embeddable/search_embeddable_transforms.test.ts b/src/platform/plugins/shared/discover/common/embeddable/search_embeddable_transforms.test.ts
index ca15bb6b3afda..78140e4f0bca6 100644
--- a/src/platform/plugins/shared/discover/common/embeddable/search_embeddable_transforms.test.ts
+++ b/src/platform/plugins/shared/discover/common/embeddable/search_embeddable_transforms.test.ts
@@ -9,7 +9,6 @@
 
 import type { DrilldownTransforms } from '@kbn/embeddable-plugin/common';
 import { getSearchEmbeddableTransforms } from './search_embeddable_transforms';
-import { extract, inject } from './search_inject_extract';
 import type {
   SearchEmbeddableByValueState,
   StoredSearchEmbeddableByValueState,
@@ -18,13 +17,6 @@ import type {
   SearchEmbeddableState,
 } from './types';
 
-jest.mock('./search_inject_extract', () => {
-  return {
-    inject: jest.fn((state, references) => state),
-    extract: jest.fn((state) => ({ state, references: [] })),
-  };
-});
-
 const mockDrilldownTransforms = {
   transformIn: jest.fn().mockImplementation((state: SearchEmbeddableState) => ({
     state,
@@ -82,10 +74,6 @@ describe('searchEmbeddableTransforms', () => {
         state,
         references
       );
-      expect(inject).toHaveBeenCalledWith(
-        { type: 'search', ...{ ...state, attributes: expectedAttributes } },
-        references
-      );
       expect(result).toEqual({
         ...state,
         attributes: expectedAttributes,
@@ -204,7 +192,6 @@ describe('searchEmbeddableTransforms', () => {
               searchSourceJSON: '{"query":{"match_all":{}}}',
             },
             tabs: [],
-            references: [],
           },
           title: 'Panel Title',
         };
@@ -212,10 +199,6 @@ describe('searchEmbeddableTransforms', () => {
         const result =
           getSearchEmbeddableTransforms(mockDrilldownTransforms).transformIn!(serializedState);
 
-        expect(extract).toHaveBeenCalledWith({
-          type: 'search',
-          attributes: serializedState.attributes,
-        });
         expect(result.state as StoredSearchEmbeddableByValueState).toEqual(serializedState);
         expect(result.references).toEqual([]);
       });
@@ -244,10 +227,6 @@ describe('searchEmbeddableTransforms', () => {
 
         expect(result.references).toEqual([]);
         expect(mockDrilldownTransforms.transformIn).toHaveBeenCalledWith(serializedState);
-        expect(extract).toHaveBeenCalledWith({
-          type: 'search',
-          attributes: serializedState.attributes,
-        });
       });
     });
   });
diff --git a/src/platform/plugins/shared/discover/common/embeddable/search_inject_extract.test.ts b/src/platform/plugins/shared/discover/common/embeddable/search_inject_extract.test.ts
deleted file mode 100644
index aa0af9b0394f3..0000000000000
--- a/src/platform/plugins/shared/discover/common/embeddable/search_inject_extract.test.ts
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * 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", the "GNU Affero General Public License v3.0 only", and the "Server Side
- * Public License v 1"; you may not use this file except in compliance with, at
- * your election, the "Elastic License 2.0", the "GNU Affero General Public
- * License v3.0 only", or the "Server Side Public License, v 1".
- */
-
-import type { SavedSearchByValueAttributes } from '@kbn/saved-search-plugin/common';
-import { extract, inject } from './search_inject_extract';
-
-describe('search inject extract', () => {
-  describe('inject', () => {
-    it('should not inject references if state does not have attributes', () => {
-      const state = { type: 'type', id: 'id' };
-      const injectedReferences = [{ name: 'name', type: 'type', id: 'id' }];
-      expect(inject(state, injectedReferences)).toEqual(state);
-    });
-
-    it('should inject references if state has references with the same name', () => {
-      const state = {
-        type: 'type',
-        id: 'id',
-        attributes: {
-          references: [{ name: 'name', type: 'type', id: '1' }],
-        },
-      };
-      const injectedReferences = [{ name: 'name', type: 'type', id: '2' }];
-      expect(inject(state, injectedReferences)).toEqual({
-        ...state,
-        attributes: {
-          ...state.attributes,
-          references: injectedReferences,
-        },
-      });
-    });
-
-    it('should clear references if state has no references with the same name', () => {
-      const state = {
-        type: 'type',
-        id: 'id',
-        attributes: {
-          references: [{ name: 'name', type: 'type', id: '1' }],
-        },
-      };
-      const injectedReferences = [{ name: 'other', type: 'type', id: '2' }];
-      expect(inject(state, injectedReferences)).toEqual({
-        ...state,
-        attributes: {
-          ...state.attributes,
-          references: [],
-        },
-      });
-    });
-  });
-
-  describe('extract', () => {
-    it('should not extract references if state does not have attributes', () => {
-      const state = { type: 'type', id: 'id' };
-      expect(extract(state)).toEqual({ state, references: [] });
-    });
-
-    it('should extract references if state has references', () => {
-      const state = {
-        type: 'type',
-        id: 'id',
-        attributes: {
-          references: [{ name: 'name', type: 'type', id: '1' }],
-        } as SavedSearchByValueAttributes,
-      };
-      expect(extract(state)).toEqual({
-        state,
-        references: [{ name: 'name', type: 'type', id: '1' }],
-      });
-    });
-  });
-});
diff --git a/src/platform/plugins/shared/discover/common/embeddable/search_inject_extract.ts b/src/platform/plugins/shared/discover/common/embeddable/search_inject_extract.ts
deleted file mode 100644
index b3ce3529a3585..0000000000000
--- a/src/platform/plugins/shared/discover/common/embeddable/search_inject_extract.ts
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * 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", the "GNU Affero General Public License v3.0 only", and the "Server Side
- * Public License v 1"; you may not use this file except in compliance with, at
- * your election, the "Elastic License 2.0", the "GNU Affero General Public
- * License v3.0 only", or the "Server Side Public License, v 1".
- */
-
-import type { WithRequiredProperty } from '@kbn/utility-types';
-import type { SavedObjectReference } from '@kbn/core-saved-objects-server';
-import type { EmbeddableStateWithType } from '@kbn/embeddable-plugin/common';
-import type { SavedSearchByValueAttributes } from '@kbn/saved-search-plugin/common';
-
-type EmbeddableStateWithTypeAndAttributes = EmbeddableStateWithType & {
-  attributes?: SavedSearchByValueAttributes;
-};
-
-export const inject = (
-  state: EmbeddableStateWithType,
-  injectedReferences: SavedObjectReference[]
-): EmbeddableStateWithTypeAndAttributes => {
-  if (hasAttributes(state)) {
-    // Filter out references that are not in the state
-    // https://github.com/elastic/kibana/pull/119079
-    const references = state.attributes.references
-      .map((stateRef) =>
-        injectedReferences.find((injectedRef) => injectedRef.name === stateRef.name)
-      )
-      .filter(Boolean);
-
-    state = {
-      ...state,
-      attributes: {
-        ...state.attributes,
-        references,
-      },
-    } as EmbeddableStateWithTypeAndAttributes;
-  }
-
-  return state;
-};
-
-export const extract = (
-  state: EmbeddableStateWithTypeAndAttributes
-): {
-  state: EmbeddableStateWithTypeAndAttributes;
-  references: SavedObjectReference[];
-} => {
-  let references: SavedObjectReference[] = [];
-
-  if (hasAttributes(state)) {
-    references = state.attributes.references;
-  }
-
-  return { state, references };
-};
-
-const hasAttributes = (
-  state: EmbeddableStateWithType
-): state is WithRequiredProperty<EmbeddableStateWithTypeAndAttributes, 'attributes'> =>
-  'attributes' in state;
diff --git a/src/platform/plugins/shared/discover/moon.yml b/src/platform/plugins/shared/discover/moon.yml
index 1ad1f28cdd481..5c921488e4020 100644
--- a/src/platform/plugins/shared/discover/moon.yml
+++ b/src/platform/plugins/shared/discover/moon.yml
@@ -64,7 +64,6 @@ dependsOn:
   - '@kbn/unified-field-list'
   - '@kbn/cell-actions'
   - '@kbn/shared-ux-utility'
-  - '@kbn/core-saved-objects-server'
   - '@kbn/discover-utils'
   - '@kbn/search-errors'
   - '@kbn/search-response-warnings'
diff --git a/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.test.ts b/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.test.ts
index 7aa15737d5f25..f5ba30a5099f2 100644
--- a/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.test.ts
+++ b/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.test.ts
@@ -132,10 +132,8 @@ describe('Serialization utils', () => {
         serializeDynamicActions: jest.fn(),
       });
 
-      const attributes = toSavedSearchAttributes(
-        savedSearch,
-        searchSource.serialize().searchSourceJSON
-      );
+      const searchSourceJSON = JSON.stringify(searchSource.getSerializedFields());
+      const attributes = toSavedSearchAttributes(savedSearch, searchSourceJSON);
 
       expect(serializedState).toEqual({
         attributes: {
@@ -146,7 +144,6 @@ describe('Serialization utils', () => {
               id: expect.any(String),
             },
           ],
-          references: mockedSavedSearchAttributes.references,
         },
       });
     });
diff --git a/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.ts b/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.ts
index 38d7953325d5f..fd6b5b414f8c6 100644
--- a/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.ts
+++ b/src/platform/plugins/shared/discover/public/embeddable/utils/serialization_utils.ts
@@ -85,7 +85,7 @@ export const serializeState = ({
   savedObjectId?: string;
 }): SearchEmbeddableState => {
   const searchSource = savedSearch.searchSource;
-  const { searchSourceJSON, references: originalReferences } = searchSource.serialize();
+  const searchSourceJSON = JSON.stringify(searchSource.getSerializedFields());
   const savedSearchAttributes = toSavedSearchAttributes(savedSearch, searchSourceJSON);
 
   if (savedObjectId) {
@@ -110,17 +110,10 @@ export const serializeState = ({
     };
   }
 
-  const state = {
-    attributes: {
-      ...savedSearchAttributes,
-      references: originalReferences,
-    },
-  };
-
   return {
     ...serializeTitles(),
     ...serializeTimeRange(),
     ...serializeDynamicActions?.(),
-    ...state,
+    attributes: savedSearchAttributes,
   };
 };
diff --git a/src/platform/plugins/shared/discover/server/embeddable/search_embeddable_factory.ts b/src/platform/plugins/shared/discover/server/embeddable/search_embeddable_factory.ts
index 4a93f87b39954..f4beb0df760c1 100644
--- a/src/platform/plugins/shared/discover/server/embeddable/search_embeddable_factory.ts
+++ b/src/platform/plugins/shared/discover/server/embeddable/search_embeddable_factory.ts
@@ -9,10 +9,7 @@
 
 import type { EmbeddableRegistryDefinition } from '@kbn/embeddable-plugin/server';
 import { SEARCH_EMBEDDABLE_TYPE } from '@kbn/discover-utils';
-import { inject, extract } from '../../common/embeddable';
 
 export const createSearchEmbeddableFactory = (): EmbeddableRegistryDefinition => ({
   id: SEARCH_EMBEDDABLE_TYPE,
-  inject,
-  extract,
 });
diff --git a/src/platform/plugins/shared/discover/tsconfig.json b/src/platform/plugins/shared/discover/tsconfig.json
index 1e04653fbf535..8eae07f516f83 100644
--- a/src/platform/plugins/shared/discover/tsconfig.json
+++ b/src/platform/plugins/shared/discover/tsconfig.json
@@ -57,7 +57,6 @@
     "@kbn/unified-field-list",
     "@kbn/cell-actions",
     "@kbn/shared-ux-utility",
-    "@kbn/core-saved-objects-server",
     "@kbn/discover-utils",
     "@kbn/search-errors",
     "@kbn/search-response-warnings",
diff --git a/src/platform/plugins/shared/saved_search/common/types.ts b/src/platform/plugins/shared/saved_search/common/types.ts
index 190661ce2f092..ca85f572f54c6 100644
--- a/src/platform/plugins/shared/saved_search/common/types.ts
+++ b/src/platform/plugins/shared/saved_search/common/types.ts
@@ -77,7 +77,8 @@ export interface SavedSearchAttributes {
 }
 
 export type SavedSearchByValueAttributes = SavedSearchAttributes & {
-  references: Reference[];
+  /** @deprecated References are now extracted/injected by server transforms */
+  references?: Reference[];
 };
 
 /** @internal **/
diff --git a/src/platform/plugins/shared/saved_search/public/service/to_saved_search.ts b/src/platform/plugins/shared/saved_search/public/service/to_saved_search.ts
index 9844e6eb55a70..7f6338115535e 100644
--- a/src/platform/plugins/shared/saved_search/public/service/to_saved_search.ts
+++ b/src/platform/plugins/shared/saved_search/public/service/to_saved_search.ts
@@ -32,10 +32,11 @@ export const byValueToSavedSearch = async <
   serializable?: Serialized
 ): Promise<ReturnType> => {
   const { sharingSavedObjectProps, managed } = result.metaInfo ?? {};
-
+  const { references, ...attributes } = result.attributes;
   return await convertToSavedSearch(
     {
-      ...splitReferences(result.attributes),
+      attributes,
+      references: references ?? [],
       savedSearchId: undefined,
       sharingSavedObjectProps,
       managed,
@@ -44,15 +45,3 @@ export const byValueToSavedSearch = async <
     serializable
   );
 };
-
-const splitReferences = (attributes: SavedSearchByValueAttributes) => {
-  const { references, ...attrs } = attributes;
-
-  return {
-    references,
-    attributes: {
-      ...attrs,
-      description: attrs.description ?? '',
-    },
-  };
-};