diff --git a/x-pack/plugins/ml/public/application/datavisualizer/index_based/page.tsx b/x-pack/plugins/ml/public/application/datavisualizer/index_based/page.tsx
index a1882d8f65f82..cf55954110bed 100644
--- a/x-pack/plugins/ml/public/application/datavisualizer/index_based/page.tsx
+++ b/x-pack/plugins/ml/public/application/datavisualizer/index_based/page.tsx
@@ -124,8 +124,9 @@ export const Page: FC = () => {
     ML_PAGES.DATA_VISUALIZER_INDEX_VIEWER,
     restorableDefaults
   );
+  const [currentSavedSearch, setCurrentSavedSearch] = useState(mlContext.currentSavedSearch);
 
-  const { combinedQuery, currentIndexPattern, currentSavedSearch, kibanaConfig } = mlContext;
+  const { combinedQuery, currentIndexPattern, kibanaConfig } = mlContext;
   const timefilter = useTimefilter({
     timeRangeSelector: currentIndexPattern.timeFieldName !== undefined,
     autoRefreshSelector: true,
@@ -193,6 +194,12 @@ export const Page: FC = () => {
     searchString: Query['query'];
     queryLanguage: SearchQueryLanguage;
   }) => {
+    // When the user loads saved search and then clear or modify the query
+    // we should remove the saved search and replace it with the index pattern id
+    if (currentSavedSearch !== null) {
+      setCurrentSavedSearch(null);
+    }
+
     setDataVisualizerListState({
       ...dataVisualizerListState,
       searchQuery: searchParams.searchQuery,