diff --git a/.changeset/sweet-terms-exist.md b/.changeset/sweet-terms-exist.md
new file mode 100644
index 0000000000..d0603e327a
--- /dev/null
+++ b/.changeset/sweet-terms-exist.md
@@ -0,0 +1,5 @@
+---
+'@xyflow/react': patch
+---
+
+Use `useEffect` for StoreUpdater to restore previous behaviour
diff --git a/packages/react/src/components/StoreUpdater/index.tsx b/packages/react/src/components/StoreUpdater/index.tsx
index a22895a418..223e62bc27 100644
--- a/packages/react/src/components/StoreUpdater/index.tsx
+++ b/packages/react/src/components/StoreUpdater/index.tsx
@@ -3,11 +3,10 @@
  * We distinguish between values we can update directly with `useDirectStoreUpdater` (like `snapGrid`)
  * and values that have a dedicated setter function in the store (like `setNodes`).
  */
-import { useRef } from 'react';
+import { useEffect, useRef } from 'react';
 import { shallow } from 'zustand/shallow';
 import { infiniteExtent, type CoordinateExtent, mergeAriaLabelConfig, AriaLabelConfig } from '@xyflow/system';
 
-import { useIsomorphicLayoutEffect } from '../../hooks/useIsomorphicLayoutEffect';
 import { useStore, useStoreApi } from '../../hooks/useStore';
 import type { Node, Edge, ReactFlowState, ReactFlowProps, FitViewOptions } from '../../types';
 import { defaultNodeOrigin } from '../../container/ReactFlow/init-values';
@@ -126,12 +125,7 @@ export function StoreUpdater<NodeType extends Node = Node, EdgeType extends Edge
   } = useStore(selector, shallow);
   const store = useStoreApi<NodeType, EdgeType>();
 
-  // We use layout effects here so that the store is always populated before
-  // any child useEffect or useLayoutEffect fires. With regular useEffect, the
-  // cleanup calls reset() which empties the store, and child effects can run
-  // before the new mount effect repopulates it — causing children to read
-  // empty nodeLookup/nodes/edges during a <ReactFlow> remount.
-  useIsomorphicLayoutEffect(() => {
+  useEffect(() => {
     setDefaultNodesAndEdges(props.defaultNodes, props.defaultEdges);
 
     return () => {
@@ -143,7 +137,7 @@ export function StoreUpdater<NodeType extends Node = Node, EdgeType extends Edge
 
   const previousFields = useRef<Partial<StoreUpdaterProps<NodeType, EdgeType>>>(initPrevValues);
 
-  useIsomorphicLayoutEffect(
+  useEffect(
     () => {
       for (const fieldName of fieldsToTrack) {
         const fieldValue = props[fieldName];