diff --git a/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.test.tsx b/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.test.tsx
index 2c1d3290fde7f..c5b6e202d481f 100644
--- a/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.test.tsx
+++ b/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.test.tsx
@@ -227,6 +227,32 @@ describe('LensEditConfigurationFlyout', () => {
     expect(saveByRefSpy).toHaveBeenCalled();
   });
 
+  it('should call the onApplyCb callback if apply button is clicked', async () => {
+    const onApplyCbSpy = jest.fn();
+
+    renderConfigFlyout(
+      {
+        closeFlyout: jest.fn(),
+        onApplyCb: onApplyCbSpy,
+      },
+      { esql: 'from index1 | limit 10' }
+    );
+    userEvent.click(screen.getByTestId('applyFlyoutButton'));
+    expect(onApplyCbSpy).toHaveBeenCalledWith({
+      title: 'test',
+      visualizationType: 'testVis',
+      state: {
+        datasourceStates: { testDatasource: 'state' },
+        visualization: {},
+        filters: [],
+        query: { esql: 'from index1 | limit 10' },
+      },
+      filters: [],
+      query: { esql: 'from index1 | limit 10' },
+      references: [],
+    });
+  });
+
   it('should not display the editor if canEditTextBasedQuery prop is false', async () => {
     renderConfigFlyout({
       canEditTextBasedQuery: false,
diff --git a/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.tsx b/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.tsx
index 42a84dc8b2f55..6c66c463f92d4 100644
--- a/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.tsx
+++ b/x-pack/plugins/lens/public/app_plugin/shared/edit_on_the_fly/lens_configuration_flyout.tsx
@@ -239,6 +239,11 @@ export function LensEditConfigurationFlyout({
     onCancelCb,
   ]);
 
+  const textBasedMode = useMemo(
+    () => (isOfAggregateQueryType(query) ? getAggregateQueryMode(query) : undefined),
+    [query]
+  );
+
   const onApply = useCallback(() => {
     const dsStates = Object.fromEntries(
       Object.entries(datasourceStates).map(([id, ds]) => {
@@ -246,18 +251,21 @@ export function LensEditConfigurationFlyout({
         return [id, dsState];
       })
     );
-    const references = extractReferencesFromState({
-      activeDatasources: Object.keys(datasourceStates).reduce(
-        (acc, id) => ({
-          ...acc,
-          [id]: datasourceMap[id],
-        }),
-        {}
-      ),
-      datasourceStates,
-      visualizationState: visualization.state,
-      activeVisualization,
-    });
+    // as ES|QL queries are using adHoc dataviews, we don't want to pass references
+    const references = !textBasedMode
+      ? extractReferencesFromState({
+          activeDatasources: Object.keys(datasourceStates).reduce(
+            (acc, id) => ({
+              ...acc,
+              [id]: datasourceMap[id],
+            }),
+            {}
+          ),
+          datasourceStates,
+          visualizationState: visualization.state,
+          activeVisualization,
+        })
+      : [];
     const attrs = {
       ...attributes,
       state: {
@@ -289,14 +297,15 @@ export function LensEditConfigurationFlyout({
     onApplyCb?.(attrs as TypedLensByValueInput['attributes']);
     closeFlyout?.();
   }, [
-    visualization.activeId,
-    savedObjectId,
-    closeFlyout,
-    onApplyCb,
     datasourceStates,
+    textBasedMode,
     visualization.state,
+    visualization.activeId,
     activeVisualization,
     attributes,
+    savedObjectId,
+    onApplyCb,
+    closeFlyout,
     datasourceMap,
     saveByRef,
     updateByRefInput,
@@ -385,8 +394,6 @@ export function LensEditConfigurationFlyout({
     getUserMessages,
   ]);
 
-  const textBasedMode = isOfAggregateQueryType(query) ? getAggregateQueryMode(query) : undefined;
-
   if (isLoading) return null;
   // Example is the Discover editing where we dont want to render the text based editor on the panel, neither the suggestions (for now)
   if (!canEditTextBasedQuery && hidesSuggestions) {
diff --git a/x-pack/plugins/lens/public/embeddable/embeddable.tsx b/x-pack/plugins/lens/public/embeddable/embeddable.tsx
index 85cc646de3005..faa617f081d8f 100644
--- a/x-pack/plugins/lens/public/embeddable/embeddable.tsx
+++ b/x-pack/plugins/lens/public/embeddable/embeddable.tsx
@@ -792,22 +792,28 @@ export class Embeddable
         ...viz.state.datasourceStates,
         [activeDatasourceId]: datasourceState,
       };
-      const references = extractReferencesFromState({
-        activeDatasources: Object.keys(datasourceStates).reduce(
-          (acc, datasourceId) => ({
-            ...acc,
-            [datasourceId]: this.deps.datasourceMap[datasourceId],
-          }),
-          {}
-        ),
-        datasourceStates: Object.fromEntries(
-          Object.entries(datasourceStates).map(([id, state]) => [id, { isLoading: false, state }])
-        ),
-        visualizationState,
-        activeVisualization: this.activeVisualizationId
-          ? this.deps.visualizationMap[visualizationType ?? this.activeVisualizationId]
-          : undefined,
-      });
+      const references =
+        activeDatasourceId === 'formBased'
+          ? extractReferencesFromState({
+              activeDatasources: Object.keys(datasourceStates).reduce(
+                (acc, datasourceId) => ({
+                  ...acc,
+                  [datasourceId]: this.deps.datasourceMap[datasourceId],
+                }),
+                {}
+              ),
+              datasourceStates: Object.fromEntries(
+                Object.entries(datasourceStates).map(([id, state]) => [
+                  id,
+                  { isLoading: false, state },
+                ])
+              ),
+              visualizationState,
+              activeVisualization: this.activeVisualizationId
+                ? this.deps.visualizationMap[visualizationType ?? this.activeVisualizationId]
+                : undefined,
+            })
+          : [];
       const attrs = {
         ...viz,
         state: {