diff --git a/packages/react/src/store/index.ts b/packages/react/src/store/index.ts
index 0f50f385..49c7c688 100644
--- a/packages/react/src/store/index.ts
+++ b/packages/react/src/store/index.ts
@@ -2,7 +2,7 @@ import { createWithEqualityFn } from 'zustand/traditional';
 import {
   clampPosition,
   fitView as fitViewSystem,
-  updateNodes,
+  adoptUserProvidedNodes,
   updateAbsolutePositions,
   panBy as panBySystem,
   Dimensions,
@@ -42,11 +42,16 @@ const createRFStore = ({
       ...getInitialState({ nodes, edges, width, height, fitView }),
       setNodes: (nodes: Node[]) => {
         const { nodeLookup, nodeOrigin, elevateNodesOnSelect } = get();
-        // Whenver new nodes are set, we need to calculate the absolute positions of the nodes
-        // and update the nodeLookup.
-        const nextNodes = updateNodes(nodes, nodeLookup, { nodeOrigin, elevateNodesOnSelect });
+        // setNodes() is called exclusively in response to user actions:
+        // - either when the `<ReactFlow nodes>` prop is updated in the controlled ReactFlow setup,
+        // - or when the user calls something like `reactFlowInstance.setNodes()` in an uncontrolled ReactFlow setup.
+        //
+        // When this happens, we take the note objects passed by the user and extend them with fields
+        // relevant for internal React Flow operations.
+        // TODO: consider updating the types to reflect the distinction between user-provided nodes and internal nodes.
+        const nodesWithInternalData = adoptUserProvidedNodes(nodes, nodeLookup, { nodeOrigin, elevateNodesOnSelect });
 
-        set({ nodes: nextNodes });
+        set({ nodes: nodesWithInternalData });
       },
       setEdges: (edges: Edge[]) => {
         const { defaultEdgeOptions = {} } = get();
@@ -69,7 +74,7 @@ const createRFStore = ({
         };
 
         if (hasDefaultNodes) {
-          nextState.nodes = updateNodes(nodes, new Map(), {
+          nextState.nodes = adoptUserProvidedNodes(nodes, new Map(), {
             nodeOrigin: get().nodeOrigin,
             elevateNodesOnSelect: get().elevateNodesOnSelect,
           });
@@ -163,7 +168,7 @@ const createRFStore = ({
         if (changes?.length) {
           if (hasDefaultNodes) {
             const updatedNodes = applyNodeChanges(changes, nodes);
-            const nextNodes = updateNodes(updatedNodes, nodeLookup, {
+            const nextNodes = adoptUserProvidedNodes(updatedNodes, nodeLookup, {
               nodeOrigin,
               elevateNodesOnSelect,
             });
diff --git a/packages/react/src/store/initialState.ts b/packages/react/src/store/initialState.ts
index 48e5434f..d54ff61c 100644
--- a/packages/react/src/store/initialState.ts
+++ b/packages/react/src/store/initialState.ts
@@ -1,7 +1,7 @@
 import {
   infiniteExtent,
   ConnectionMode,
-  updateNodes,
+  adoptUserProvidedNodes,
   getNodesBounds,
   getViewportForBounds,
   Transform,
@@ -23,7 +23,7 @@ const getInitialState = ({
   fitView?: boolean;
 } = {}): ReactFlowStore => {
   const nodeLookup = new Map<string, Node>();
-  const nextNodes = updateNodes(nodes, nodeLookup, { nodeOrigin: [0, 0], elevateNodesOnSelect: false });
+  const nextNodes = adoptUserProvidedNodes(nodes, nodeLookup, { nodeOrigin: [0, 0], elevateNodesOnSelect: false });
 
   let transform: Transform = [0, 0, 1];
 
diff --git a/packages/svelte/src/lib/store/initial-store.ts b/packages/svelte/src/lib/store/initial-store.ts
index dbbb17fc..a3ac2f1e 100644
--- a/packages/svelte/src/lib/store/initial-store.ts
+++ b/packages/svelte/src/lib/store/initial-store.ts
@@ -15,7 +15,7 @@ import {
   type OnError,
   devWarn,
   type Viewport,
-  updateNodes,
+  adoptUserProvidedNodes,
   getNodesBounds,
   getViewportForBounds
 } from '@xyflow/system';
@@ -68,7 +68,7 @@ export const getInitialStore = ({
   fitView?: boolean;
 }) => {
   const nodeLookup = new Map<string, Node>();
-  const nextNodes = updateNodes(nodes, nodeLookup, {
+  const nextNodes = adoptUserProvidedNodes(nodes, nodeLookup, {
     nodeOrigin: [0, 0],
     elevateNodesOnSelect: false
   });
diff --git a/packages/svelte/src/lib/store/utils.ts b/packages/svelte/src/lib/store/utils.ts
index a11bf1f6..2d53ac90 100644
--- a/packages/svelte/src/lib/store/utils.ts
+++ b/packages/svelte/src/lib/store/utils.ts
@@ -6,7 +6,7 @@ import {
   type Writable,
   get
 } from 'svelte/store';
-import { updateNodes, type Viewport, type PanZoomInstance } from '@xyflow/system';
+import { adoptUserProvidedNodes, type Viewport, type PanZoomInstance } from '@xyflow/system';
 
 import type { DefaultEdgeOptions, DefaultNodeOptions, Edge, Node } from '$lib/types';
 
@@ -133,7 +133,7 @@ export const createNodesStore = (
   let elevateNodesOnSelect = true;
 
   const _set = (nds: Node[]): Node[] => {
-    const nextNodes = updateNodes(nds, nodeLookup, {
+    const nextNodes = adoptUserProvidedNodes(nds, nodeLookup, {
       elevateNodesOnSelect,
       defaults
     });
diff --git a/packages/system/src/types/nodes.ts b/packages/system/src/types/nodes.ts
index b55f3f54..33884bf7 100644
--- a/packages/system/src/types/nodes.ts
+++ b/packages/system/src/types/nodes.ts
@@ -40,6 +40,10 @@ export type NodeBase<T = any, U extends string | undefined = string | undefined>
     z?: number;
     handleBounds?: NodeHandleBounds;
     isParent?: boolean;
+    /** Holds a reference to the original node object provided by the user
+     * (which may lack some fields, like `computed` or `[internalSymbol]`. Used
+     * as an optimization to avoid certain operations. */
+    userProvidedNode: WeakRef<NodeBase>;
   };
 };
 
diff --git a/packages/system/src/utils/store.ts b/packages/system/src/utils/store.ts
index eca6b8de..34d3d529 100644
--- a/packages/system/src/utils/store.ts
+++ b/packages/system/src/utils/store.ts
@@ -62,7 +62,7 @@ type UpdateNodesOptions<NodeType extends NodeBase> = {
   defaults?: Partial<NodeType>;
 };
 
-export function updateNodes<NodeType extends NodeBase>(
+export function adoptUserProvidedNodes<NodeType extends NodeBase>(
   nodes: NodeType[],
   nodeLookup: Map<string, NodeType>,
   options: UpdateNodesOptions<NodeType> = {
@@ -76,6 +76,8 @@ export function updateNodes<NodeType extends NodeBase>(
 
   const nextNodes = nodes.map((n) => {
     const currentStoreNode = nodeLookup.get(n.id);
+    if (n === currentStoreNode?.[internalsSymbol]?.userProvidedNode.deref()) return currentStoreNode;
+
     const node: NodeType = {
       ...options.defaults,
       ...n,
@@ -97,6 +99,7 @@ export function updateNodes<NodeType extends NodeBase>(
       value: {
         handleBounds: currInternals?.handleBounds,
         z,
+        userProvidedNode: new WeakRef(n),
       },
     });