diff --git a/.changeset/good-lamps-think.md b/.changeset/good-lamps-think.md
new file mode 100644
index 000000000..fa33aaa46
--- /dev/null
+++ b/.changeset/good-lamps-think.md
@@ -0,0 +1,5 @@
+---
+'@xyflow/react': patch
+---
+
+Ensure visual nodes selection state is cleared when zero selected nodes remain in the flow
diff --git a/packages/react/src/store/index.ts b/packages/react/src/store/index.ts
index 5ca9bac2e..895719ef6 100644
--- a/packages/react/src/store/index.ts
+++ b/packages/react/src/store/index.ts
@@ -97,7 +97,16 @@ const createStore = ({
         zIndexMode,
       }),
       setNodes: (nodes: Node[]) => {
-        const { nodeLookup, parentLookup, nodeOrigin, elevateNodesOnSelect, fitViewQueued, zIndexMode } = get();
+        const {
+          nodeLookup,
+          parentLookup,
+          nodeOrigin,
+          elevateNodesOnSelect,
+          fitViewQueued,
+          zIndexMode,
+          nodesSelectionActive,
+        } = get();
+
         /*
          * setNodes() is called exclusively in response to user actions:
          * - either when the `<ReactFlow nodes>` prop is updated in the controlled ReactFlow setup,
@@ -107,7 +116,7 @@ const createStore = ({
          * relevant for internal React Flow operations.
          */
 
-        const nodesInitialized = adoptUserNodes(nodes, nodeLookup, parentLookup, {
+        const { nodesInitialized, hasSelectedNodes } = adoptUserNodes(nodes, nodeLookup, parentLookup, {
           nodeOrigin,
           nodeExtent,
           elevateNodesOnSelect,
@@ -115,11 +124,19 @@ const createStore = ({
           zIndexMode,
         });
 
+        const nextNodesSelectionActive = nodesSelectionActive && hasSelectedNodes;
+
         if (fitViewQueued && nodesInitialized) {
           resolveFitView();
-          set({ nodes, nodesInitialized, fitViewQueued: false, fitViewOptions: undefined });
+          set({
+            nodes,
+            nodesInitialized,
+            fitViewQueued: false,
+            fitViewOptions: undefined,
+            nodesSelectionActive: nextNodesSelectionActive
+          });
         } else {
-          set({ nodes, nodesInitialized });
+          set({ nodes, nodesInitialized, nodesSelectionActive: nextNodesSelectionActive });
         }
       },
       setEdges: (edges: Edge[]) => {
diff --git a/packages/react/src/store/initialState.ts b/packages/react/src/store/initialState.ts
index 26a5c045d..53470d11a 100644
--- a/packages/react/src/store/initialState.ts
+++ b/packages/react/src/store/initialState.ts
@@ -56,7 +56,7 @@ const getInitialState = ({
   const storeNodeExtent = nodeExtent ?? infiniteExtent;
 
   updateConnectionLookup(connectionLookup, edgeLookup, storeEdges);
-  const nodesInitialized = adoptUserNodes(storeNodes, nodeLookup, parentLookup, {
+  const { nodesInitialized } = adoptUserNodes(storeNodes, nodeLookup, parentLookup, {
     nodeOrigin: storeNodeOrigin,
     nodeExtent: storeNodeExtent,
     zIndexMode,
diff --git a/packages/svelte/src/lib/store/initial-store.svelte.ts b/packages/svelte/src/lib/store/initial-store.svelte.ts
index 515d1dabc..62165d46b 100644
--- a/packages/svelte/src/lib/store/initial-store.svelte.ts
+++ b/packages/svelte/src/lib/store/initial-store.svelte.ts
@@ -120,7 +120,7 @@ export function getInitialStore<NodeType extends Node = Node, EdgeType extends E
     zIndexMode = $state.raw<ZIndexMode>(signals.props.zIndexMode ?? 'basic');
 
     nodesInitialized: boolean = $derived.by(() => {
-      const nodesInitialized = adoptUserNodes(signals.nodes, this.nodeLookup, this.parentLookup, {
+      const { nodesInitialized } = adoptUserNodes(signals.nodes, this.nodeLookup, this.parentLookup, {
         nodeExtent: this.nodeExtent,
         nodeOrigin: this.nodeOrigin,
         elevateNodesOnSelect: signals.props.elevateNodesOnSelect ?? true,
diff --git a/packages/system/src/utils/store.ts b/packages/system/src/utils/store.ts
index 2bae20c85..114133899 100644
--- a/packages/system/src/utils/store.ts
+++ b/packages/system/src/utils/store.ts
@@ -121,18 +121,24 @@ export function isManualZIndexMode(zIndexMode?: ZIndexMode): boolean {
   return zIndexMode === 'manual';
 }
 
+type AdoptUserNodesReturn = {
+  nodesInitialized: boolean;
+  hasSelectedNodes: boolean;
+};
+
 export function adoptUserNodes<NodeType extends NodeBase>(
   nodes: NodeType[],
   nodeLookup: NodeLookup<InternalNodeBase<NodeType>>,
   parentLookup: ParentLookup<InternalNodeBase<NodeType>>,
   options: UpdateNodesOptions<NodeType> = {}
-): boolean {
+): AdoptUserNodesReturn {
   const _options = mergeObjects(adoptUserNodesDefaultOptions, options);
   const rootParentIndex = { i: 0 };
   const tmpLookup = new Map(nodeLookup);
   const selectedNodeZ: number =
     _options?.elevateNodesOnSelect && !isManualZIndexMode(_options.zIndexMode) ? SELECTED_NODE_Z : 0;
   let nodesInitialized = nodes.length > 0;
+  let hasSelectedNodes = false;
 
   nodeLookup.clear();
   parentLookup.clear();
@@ -178,9 +184,11 @@ export function adoptUserNodes<NodeType extends NodeBase>(
     if (userNode.parentId) {
       updateChildNode(internalNode, nodeLookup, parentLookup, options, rootParentIndex);
     }
+
+    hasSelectedNodes ||= userNode.selected ?? false;
   }
 
-  return nodesInitialized;
+  return { nodesInitialized, hasSelectedNodes };
 }
 
 function updateParentLookup<NodeType extends NodeBase>(