diff --git a/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_edit.tsx b/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_edit.tsx
index c9641deb4f2fc..8091e64e715cf 100644
--- a/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_edit.tsx
+++ b/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_edit.tsx
@@ -37,6 +37,7 @@ import { setupPanelManagement } from '../inline_editing/panel_management';
 import { mountInlineEditPanel } from '../inline_editing/mount';
 import { StateManagementConfig } from './initialize_state_management';
 import { apiPublishesInlineEditingCapabilities } from '../type_guards';
+import { SearchContextConfig } from './initialize_search_context';
 
 function getSupportedTriggers(
   getState: GetStateType,
@@ -61,6 +62,7 @@ export function initializeEditApi(
   internalApi: LensInternalApi,
   stateApi: StateManagementConfig['api'],
   inspectorApi: LensInspectorAdapters,
+  searchContextApi: SearchContextConfig['api'],
   isTextBasedLanguage: (currentState: LensRuntimeState) => boolean,
   startDependencies: LensEmbeddableStartServices,
   parentApi?: unknown
@@ -126,9 +128,34 @@ export function initializeEditApi(
     stateApi.updateSavedObjectId(newState.savedObjectId);
   };
 
+  // Wrap the getState() when inline editing and make sure that the filters in the attributes
+  // are properly injected with the correct references to avoid issues when saving/navigating to the full editor
+  const getStateWithInjectedFilters = () => {
+    const currentState = getState();
+    // use the search context api here for filters for 2 reasons:
+    // * the filters here have the correct references already injected
+    // * the edit filters flow may change in the future and this is the right place to get the filters
+    const currentFilters = searchContextApi.filters$.getValue() ?? [];
+    // if there are no filters, avoid to copy the attributes
+    if (!currentFilters.length) {
+      return currentState;
+    }
+    // otherwise make sure to inject the references into filters
+    return {
+      ...currentState,
+      attributes: {
+        ...currentState.attributes,
+        state: {
+          ...currentState.attributes.state,
+          filters: currentFilters,
+        },
+      },
+    };
+  };
+
   const openInlineEditor = prepareInlineEditPanel(
     initialState,
-    getState,
+    getStateWithInjectedFilters,
     updateState,
     internalApi,
     panelManagementApi,
@@ -206,6 +233,9 @@ export function initializeEditApi(
         const rootEmbeddable = parentApi;
         const overlayTracker = tracksOverlays(rootEmbeddable) ? rootEmbeddable : undefined;
         const ConfigPanel = await openInlineEditor({
+          // the getState() here contains the wrong filters references
+          // but the input attributes are correct as openInlineEditor() handler is using
+          // the getStateWithInjectedFilters() function
           onApply: (attributes: LensRuntimeState['attributes']) =>
             updateState({ ...getState(), attributes }),
           // restore the first state found when the panel opened
diff --git a/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_search_context.ts b/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_search_context.ts
index 1a608de11e230..1d95fd49b3f55 100644
--- a/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_search_context.ts
+++ b/x-pack/plugins/lens/public/react_embeddable/initializers/initialize_search_context.ts
@@ -18,18 +18,26 @@ import {
   apiPublishesSearchSession,
 } from '@kbn/presentation-publishing/interfaces/fetch/publishes_search_session';
 import { buildObservableVariable } from '../helper';
-import { LensInternalApi, LensRuntimeState, LensUnifiedSearchContext } from '../types';
+import {
+  LensEmbeddableStartServices,
+  LensInternalApi,
+  LensRuntimeState,
+  LensUnifiedSearchContext,
+} from '../types';
 
-export function initializeSearchContext(
-  initialState: LensRuntimeState,
-  internalApi: LensInternalApi,
-  parentApi: unknown
-): {
+export interface SearchContextConfig {
   api: PublishesUnifiedSearch & PublishesSearchSession;
   comparators: StateComparators<LensUnifiedSearchContext>;
   serialize: () => LensUnifiedSearchContext;
   cleanup: () => void;
-} {
+}
+
+export function initializeSearchContext(
+  initialState: LensRuntimeState,
+  internalApi: LensInternalApi,
+  parentApi: unknown,
+  { injectFilterReferences }: LensEmbeddableStartServices
+): SearchContextConfig {
   const [searchSessionId$] = buildObservableVariable<string | undefined>(
     apiPublishesSearchSession(parentApi) ? parentApi.searchSessionId$ : undefined
   );
@@ -38,7 +46,10 @@ export function initializeSearchContext(
 
   const [lastReloadRequestTime] = buildObservableVariable<number | undefined>(undefined);
 
-  const [filters$] = buildObservableVariable<Filter[] | undefined>(attributes.state.filters);
+  // Make sure the panel access the filters with the correct references
+  const [filters$] = buildObservableVariable<Filter[] | undefined>(
+    injectFilterReferences(attributes.state.filters, attributes.references)
+  );
 
   const [query$] = buildObservableVariable<Query | AggregateQuery | undefined>(
     attributes.state.query
diff --git a/x-pack/plugins/lens/public/react_embeddable/lens_embeddable.tsx b/x-pack/plugins/lens/public/react_embeddable/lens_embeddable.tsx
index 2fc1928dc40c8..c193e02c06f0e 100644
--- a/x-pack/plugins/lens/public/react_embeddable/lens_embeddable.tsx
+++ b/x-pack/plugins/lens/public/react_embeddable/lens_embeddable.tsx
@@ -84,6 +84,13 @@ export const createLensEmbeddableFactory = (
 
       const inspectorConfig = initializeInspector(services);
 
+      const searchContextConfig = initializeSearchContext(
+        initialState,
+        internalApi,
+        parentApi,
+        services
+      );
+
       const editConfig = initializeEditApi(
         uuid,
         initialState,
@@ -91,12 +98,12 @@ export const createLensEmbeddableFactory = (
         internalApi,
         stateConfig.api,
         inspectorConfig.api,
+        searchContextConfig.api,
         isTextBasedLanguage,
         services,
         parentApi
       );
 
-      const searchContextConfig = initializeSearchContext(initialState, internalApi, parentApi);
       const integrationsConfig = initializeIntegrations(getState, services);
       const actionsConfig = initializeActionApi(
         uuid,