diff --git a/src/renderer/core/layout/store/layoutStore.ts b/src/renderer/core/layout/store/layoutStore.ts
index 15d4128142..f32a101f74 100644
--- a/src/renderer/core/layout/store/layoutStore.ts
+++ b/src/renderer/core/layout/store/layoutStore.ts
@@ -10,6 +10,7 @@ import * as Y from 'yjs'
 
 import { ACTOR_CONFIG } from '@/renderer/core/layout/constants'
 import type {
+  BatchUpdateBoundsOperation,
   CreateLinkOperation,
   CreateNodeOperation,
   CreateRerouteOperation,
@@ -864,6 +865,12 @@ class LayoutStoreImpl implements LayoutStore {
       case 'deleteNode':
         this.handleDeleteNode(operation as DeleteNodeOperation, change)
         break
+      case 'batchUpdateBounds':
+        this.handleBatchUpdateBounds(
+          operation as BatchUpdateBoundsOperation,
+          change
+        )
+        break
       case 'createLink':
         this.handleCreateLink(operation as CreateLinkOperation, change)
         break
@@ -1092,6 +1099,38 @@ class LayoutStoreImpl implements LayoutStore {
     change.nodeIds.push(operation.nodeId)
   }
 
+  private handleBatchUpdateBounds(
+    operation: BatchUpdateBoundsOperation,
+    change: LayoutChange
+  ): void {
+    const spatialUpdates: Array<{ nodeId: NodeId; bounds: Bounds }> = []
+
+    for (const nodeId of operation.nodeIds) {
+      const data = operation.bounds[nodeId]
+      const ynode = this.ynodes.get(nodeId)
+      if (!ynode || !data) continue
+
+      ynode.set('position', { x: data.bounds.x, y: data.bounds.y })
+      ynode.set('size', {
+        width: data.bounds.width,
+        height: data.bounds.height
+      })
+      ynode.set('bounds', data.bounds)
+
+      spatialUpdates.push({ nodeId, bounds: data.bounds })
+      change.nodeIds.push(nodeId)
+    }
+
+    // Batch update spatial index for better performance
+    if (spatialUpdates.length > 0) {
+      this.spatialIndex.batchUpdate(spatialUpdates)
+    }
+
+    if (change.nodeIds.length) {
+      change.type = 'update'
+    }
+  }
+
   private handleCreateLink(
     operation: CreateLinkOperation,
     change: LayoutChange
@@ -1372,19 +1411,38 @@ class LayoutStoreImpl implements LayoutStore {
     const originalSource = this.currentSource
     this.currentSource = LayoutSource.Vue
 
-    this.ydoc.transact(() => {
-      for (const { nodeId, bounds } of updates) {
-        const ynode = this.ynodes.get(nodeId)
-        if (!ynode) continue
+    const nodeIds: NodeId[] = []
+    const boundsRecord: BatchUpdateBoundsOperation['bounds'] = {}
 
-        this.spatialIndex.update(nodeId, bounds)
-        ynode.set('bounds', bounds)
-        ynode.set('position', { x: bounds.x, y: bounds.y })
-        ynode.set('size', { width: bounds.width, height: bounds.height })
+    for (const { nodeId, bounds } of updates) {
+      const ynode = this.ynodes.get(nodeId)
+      if (!ynode) continue
+      const currentLayout = yNodeToLayout(ynode)
+
+      boundsRecord[nodeId] = {
+        bounds,
+        previousBounds: currentLayout.bounds
       }
-    }, this.currentActor)
+      nodeIds.push(nodeId)
+    }
+
+    if (!nodeIds.length) {
+      this.currentSource = originalSource
+      return
+    }
+
+    const operation: BatchUpdateBoundsOperation = {
+      type: 'batchUpdateBounds',
+      entity: 'node',
+      nodeIds,
+      bounds: boundsRecord,
+      timestamp: Date.now(),
+      source: this.currentSource,
+      actor: this.currentActor
+    }
+
+    this.applyOperation(operation)
 
-    // Restore original source
     this.currentSource = originalSource
   }
 }
diff --git a/src/renderer/core/layout/sync/useLinkLayoutSync.ts b/src/renderer/core/layout/sync/useLinkLayoutSync.ts
index 565022582d..b1cbc5fa0b 100644
--- a/src/renderer/core/layout/sync/useLinkLayoutSync.ts
+++ b/src/renderer/core/layout/sync/useLinkLayoutSync.ts
@@ -267,6 +267,11 @@ export function useLinkLayoutSync() {
           case 'resizeNode':
             recomputeLinksForNode(parseInt(change.operation.nodeId))
             break
+          case 'batchUpdateBounds':
+            for (const nodeId of change.operation.nodeIds) {
+              recomputeLinksForNode(parseInt(nodeId))
+            }
+            break
           case 'createLink':
             recomputeLinkById(change.operation.linkId)
             break
diff --git a/src/renderer/core/layout/types.ts b/src/renderer/core/layout/types.ts
index ae2b761398..5703751284 100644
--- a/src/renderer/core/layout/types.ts
+++ b/src/renderer/core/layout/types.ts
@@ -122,7 +122,7 @@ type OperationType =
   | 'createNode'
   | 'deleteNode'
   | 'setNodeVisibility'
-  | 'batchUpdate'
+  | 'batchUpdateBounds'
   | 'createLink'
   | 'deleteLink'
   | 'createReroute'
@@ -184,10 +184,11 @@ interface SetNodeVisibilityOperation extends NodeOpBase {
 /**
  * Batch update operation for atomic multi-property changes
  */
-interface BatchUpdateOperation extends NodeOpBase {
-  type: 'batchUpdate'
-  updates: Partial<NodeLayout>
-  previousValues: Partial<NodeLayout>
+export interface BatchUpdateBoundsOperation extends OperationMeta {
+  entity: 'node'
+  type: 'batchUpdateBounds'
+  nodeIds: NodeId[]
+  bounds: Record<NodeId, { bounds: Bounds; previousBounds: Bounds }>
 }
 
 /**
@@ -244,7 +245,7 @@ export type LayoutOperation =
   | CreateNodeOperation
   | DeleteNodeOperation
   | SetNodeVisibilityOperation
-  | BatchUpdateOperation
+  | BatchUpdateBoundsOperation
   | CreateLinkOperation
   | DeleteLinkOperation
   | CreateRerouteOperation
diff --git a/src/renderer/core/spatial/SpatialIndex.ts b/src/renderer/core/spatial/SpatialIndex.ts
index 92a4a627f9..8541352c1c 100644
--- a/src/renderer/core/spatial/SpatialIndex.ts
+++ b/src/renderer/core/spatial/SpatialIndex.ts
@@ -55,6 +55,17 @@ export class SpatialIndexManager {
     this.invalidateCache()
   }
 
+  /**
+   * Batch update multiple nodes' bounds in the spatial index
+   * More efficient than calling update() multiple times as it only invalidates cache once
+   */
+  batchUpdate(updates: Array<{ nodeId: NodeId; bounds: Bounds }>): void {
+    for (const { nodeId, bounds } of updates) {
+      this.quadTree.update(nodeId, bounds)
+    }
+    this.invalidateCache()
+  }
+
   /**
    * Remove a node from the spatial index
    */
diff --git a/src/renderer/extensions/vueNodes/components/LGraphNode.vue b/src/renderer/extensions/vueNodes/components/LGraphNode.vue
index 1213936cb9..54d8f6948a 100644
--- a/src/renderer/extensions/vueNodes/components/LGraphNode.vue
+++ b/src/renderer/extensions/vueNodes/components/LGraphNode.vue
@@ -153,6 +153,7 @@ import {
 import { cn } from '@/utils/tailwindUtil'
 
 import { useNodeResize } from '../composables/useNodeResize'
+import { calculateIntrinsicSize } from '../utils/calculateIntrinsicSize'
 import NodeContent from './NodeContent.vue'
 import NodeHeader from './NodeHeader.vue'
 import NodeSlots from './NodeSlots.vue'
@@ -245,7 +246,7 @@ onErrorCaptured((error) => {
 })
 
 // Use layout system for node position and dragging
-const { position, size, zIndex, resize } = useNodeLayout(() => nodeData.id)
+const { position, size, zIndex } = useNodeLayout(() => nodeData.id)
 const { pointerHandlers, isDragging, dragStyle } = useNodePointerInteractions(
   () => nodeData,
   handleNodeSelect
@@ -267,13 +268,19 @@ const handleContextMenu = (event: MouseEvent) => {
 }
 
 onMounted(() => {
-  if (size.value && transformState?.camera) {
-    const scale = transformState.camera.z
-    const screenSize = {
-      width: size.value.width * scale,
-      height: size.value.height * scale
-    }
-    resize(screenSize)
+  // Set initial DOM size from layout store, but respect intrinsic content minimum
+  if (size.value && nodeContainerRef.value && transformState) {
+    const intrinsicMin = calculateIntrinsicSize(
+      nodeContainerRef.value,
+      transformState.camera.z
+    )
+
+    // Use the larger of stored size or intrinsic minimum
+    const finalWidth = Math.max(size.value.width, intrinsicMin.width)
+    const finalHeight = Math.max(size.value.height, intrinsicMin.height)
+
+    nodeContainerRef.value.style.width = `${finalWidth}px`
+    nodeContainerRef.value.style.height = `${finalHeight}px`
   }
 })
 
diff --git a/src/renderer/extensions/vueNodes/composables/useNodeResize.ts b/src/renderer/extensions/vueNodes/composables/useNodeResize.ts
index a216646e23..4cecefc67b 100644
--- a/src/renderer/extensions/vueNodes/composables/useNodeResize.ts
+++ b/src/renderer/extensions/vueNodes/composables/useNodeResize.ts
@@ -2,6 +2,7 @@ import { useEventListener } from '@vueuse/core'
 import { ref } from 'vue'
 
 import type { TransformState } from '@/renderer/core/layout/injectionKeys'
+import { calculateIntrinsicSize } from '@/renderer/extensions/vueNodes/utils/calculateIntrinsicSize'
 
 interface Size {
   width: number
@@ -53,29 +54,16 @@ export function useNodeResize(
     if (!(nodeElement instanceof HTMLElement)) return
 
     const rect = nodeElement.getBoundingClientRect()
-
-    // Calculate intrinsic content size once at start
-    const originalWidth = nodeElement.style.width
-    const originalHeight = nodeElement.style.height
-    nodeElement.style.width = 'auto'
-    nodeElement.style.height = 'auto'
-
-    const intrinsicRect = nodeElement.getBoundingClientRect()
-
-    // Restore original size
-    nodeElement.style.width = originalWidth
-    nodeElement.style.height = originalHeight
-
-    // Convert to canvas coordinates using transform state
     const scale = transformState.camera.z
+
+    // Calculate current size in canvas coordinates
     resizeStartSize.value = {
       width: rect.width / scale,
       height: rect.height / scale
     }
-    intrinsicMinSize.value = {
-      width: intrinsicRect.width / scale,
-      height: intrinsicRect.height / scale
-    }
+
+    // Calculate intrinsic content size (minimum based on content)
+    intrinsicMinSize.value = calculateIntrinsicSize(nodeElement, scale)
 
     const handlePointerMove = (moveEvent: PointerEvent) => {
       if (
diff --git a/src/renderer/extensions/vueNodes/layout/useNodeLayout.ts b/src/renderer/extensions/vueNodes/layout/useNodeLayout.ts
index 052c7c1b0a..2ecbd32d90 100644
--- a/src/renderer/extensions/vueNodes/layout/useNodeLayout.ts
+++ b/src/renderer/extensions/vueNodes/layout/useNodeLayout.ts
@@ -167,14 +167,6 @@ export function useNodeLayout(nodeIdMaybe: MaybeRefOrGetter<string>) {
     mutations.moveNode(nodeId, position)
   }
 
-  /**
-   * Update node size
-   */
-  function resize(newSize: { width: number; height: number }) {
-    mutations.setSource(LayoutSource.Vue)
-    mutations.resizeNode(nodeId, newSize)
-  }
-
   return {
     // Reactive state (via customRef)
     layoutRef,
@@ -187,7 +179,6 @@ export function useNodeLayout(nodeIdMaybe: MaybeRefOrGetter<string>) {
 
     // Mutations
     moveTo,
-    resize,
 
     // Drag handlers
     startDrag,
diff --git a/src/renderer/extensions/vueNodes/utils/calculateIntrinsicSize.test.ts b/src/renderer/extensions/vueNodes/utils/calculateIntrinsicSize.test.ts
new file mode 100644
index 0000000000..cd34f8a3fb
--- /dev/null
+++ b/src/renderer/extensions/vueNodes/utils/calculateIntrinsicSize.test.ts
@@ -0,0 +1,138 @@
+import { afterEach, beforeEach, describe, expect, it } from 'vitest'
+
+import { calculateIntrinsicSize } from './calculateIntrinsicSize'
+
+describe('calculateIntrinsicSize', () => {
+  let element: HTMLElement
+
+  beforeEach(() => {
+    // Create a test element
+    element = document.createElement('div')
+    element.style.width = '200px'
+    element.style.height = '100px'
+    document.body.appendChild(element)
+  })
+
+  afterEach(() => {
+    document.body.removeChild(element)
+  })
+
+  it('should calculate intrinsic size and convert to canvas coordinates', () => {
+    // Mock getBoundingClientRect to return specific dimensions
+    const originalGetBoundingClientRect = element.getBoundingClientRect
+    element.getBoundingClientRect = () => ({
+      width: 300,
+      height: 150,
+      top: 0,
+      left: 0,
+      bottom: 150,
+      right: 300,
+      x: 0,
+      y: 0,
+      toJSON: () => ({})
+    })
+
+    const scale = 2
+    const result = calculateIntrinsicSize(element, scale)
+
+    // Should divide by scale to convert from screen to canvas coordinates
+    expect(result).toEqual({
+      width: 150, // 300 / 2
+      height: 75 // 150 / 2
+    })
+
+    element.getBoundingClientRect = originalGetBoundingClientRect
+  })
+
+  it('should restore original size after measuring', () => {
+    const originalWidth = element.style.width
+    const originalHeight = element.style.height
+
+    element.getBoundingClientRect = () => ({
+      width: 300,
+      height: 150,
+      top: 0,
+      left: 0,
+      bottom: 150,
+      right: 300,
+      x: 0,
+      y: 0,
+      toJSON: () => ({})
+    })
+
+    calculateIntrinsicSize(element, 1)
+
+    // Should restore original styles
+    expect(element.style.width).toBe(originalWidth)
+    expect(element.style.height).toBe(originalHeight)
+  })
+
+  it('should handle scale of 1 correctly', () => {
+    element.getBoundingClientRect = () => ({
+      width: 400,
+      height: 200,
+      top: 0,
+      left: 0,
+      bottom: 200,
+      right: 400,
+      x: 0,
+      y: 0,
+      toJSON: () => ({})
+    })
+
+    const result = calculateIntrinsicSize(element, 1)
+
+    expect(result).toEqual({
+      width: 400,
+      height: 200
+    })
+  })
+
+  it('should handle fractional scales', () => {
+    element.getBoundingClientRect = () => ({
+      width: 300,
+      height: 150,
+      top: 0,
+      left: 0,
+      bottom: 150,
+      right: 300,
+      x: 0,
+      y: 0,
+      toJSON: () => ({})
+    })
+
+    const result = calculateIntrinsicSize(element, 0.5)
+
+    expect(result).toEqual({
+      width: 600, // 300 / 0.5
+      height: 300 // 150 / 0.5
+    })
+  })
+
+  it('should temporarily set width and height to auto during measurement', () => {
+    let widthDuringMeasurement = ''
+    let heightDuringMeasurement = ''
+
+    element.getBoundingClientRect = function (this: HTMLElement) {
+      widthDuringMeasurement = this.style.width
+      heightDuringMeasurement = this.style.height
+      return {
+        width: 300,
+        height: 150,
+        top: 0,
+        left: 0,
+        bottom: 150,
+        right: 300,
+        x: 0,
+        y: 0,
+        toJSON: () => ({})
+      }
+    }
+
+    calculateIntrinsicSize(element, 1)
+
+    // During measurement, styles should be set to 'auto'
+    expect(widthDuringMeasurement).toBe('auto')
+    expect(heightDuringMeasurement).toBe('auto')
+  })
+})
diff --git a/src/renderer/extensions/vueNodes/utils/calculateIntrinsicSize.ts b/src/renderer/extensions/vueNodes/utils/calculateIntrinsicSize.ts
new file mode 100644
index 0000000000..36da7cd827
--- /dev/null
+++ b/src/renderer/extensions/vueNodes/utils/calculateIntrinsicSize.ts
@@ -0,0 +1,34 @@
+/**
+ * Calculate the intrinsic (minimum content-based) size of a node element
+ *
+ * Temporarily sets the element to auto-size to measure its natural content dimensions,
+ * then converts from screen coordinates to canvas coordinates using the camera scale.
+ *
+ * @param element - The node element to measure
+ * @param scale - Camera zoom scale for coordinate conversion
+ * @returns The intrinsic minimum size in canvas coordinates
+ */
+export function calculateIntrinsicSize(
+  element: HTMLElement,
+  scale: number
+): { width: number; height: number } {
+  // Store original size to restore later
+  const originalWidth = element.style.width
+  const originalHeight = element.style.height
+
+  // Temporarily set to auto to measure natural content size
+  element.style.width = 'auto'
+  element.style.height = 'auto'
+
+  const intrinsicRect = element.getBoundingClientRect()
+
+  // Restore original size
+  element.style.width = originalWidth
+  element.style.height = originalHeight
+
+  // Convert from screen coordinates to canvas coordinates
+  return {
+    width: intrinsicRect.width / scale,
+    height: intrinsicRect.height / scale
+  }
+}
diff --git a/tests-ui/tests/renderer/core/layout/layoutStore.test.ts b/tests-ui/tests/renderer/core/layout/layoutStore.test.ts
index db3f9960d5..993bde8664 100644
--- a/tests-ui/tests/renderer/core/layout/layoutStore.test.ts
+++ b/tests-ui/tests/renderer/core/layout/layoutStore.test.ts
@@ -1,4 +1,4 @@
-import { beforeEach, describe, expect, it } from 'vitest'
+import { beforeEach, describe, expect, it, vi } from 'vitest'
 
 import { layoutStore } from '@/renderer/core/layout/store/layoutStore'
 import {
@@ -165,10 +165,11 @@ describe('layoutStore CRDT operations', () => {
       actor: layoutStore.getCurrentActor()
     })
 
-    // Wait for async notification
-    await new Promise((resolve) => setTimeout(resolve, 50))
+    // Wait for onChange callback to be called (uses setTimeout internally)
+    await vi.waitFor(() => {
+      expect(changes.length).toBeGreaterThanOrEqual(1)
+    })
 
-    expect(changes.length).toBeGreaterThanOrEqual(1)
     const lastChange = changes[changes.length - 1]
     expect(lastChange.source).toBe('vue')
     expect(lastChange.operation.actor).toBe('user-123')
@@ -176,6 +177,48 @@ describe('layoutStore CRDT operations', () => {
     unsubscribe()
   })
 
+  it('should emit change when batch updating node bounds', async () => {
+    const nodeId = 'test-node-6'
+    const layout = createTestNode(nodeId)
+
+    layoutStore.applyOperation({
+      type: 'createNode',
+      entity: 'node',
+      nodeId,
+      layout,
+      timestamp: Date.now(),
+      source: LayoutSource.External,
+      actor: 'test'
+    })
+
+    const changes: LayoutChange[] = []
+    const unsubscribe = layoutStore.onChange((change) => {
+      changes.push(change)
+    })
+
+    const newBounds = { x: 40, y: 60, width: 220, height: 120 }
+    layoutStore.batchUpdateNodeBounds([{ nodeId, bounds: newBounds }])
+
+    // Wait for onChange callback to be called (uses setTimeout internally)
+    await vi.waitFor(() => {
+      expect(changes.length).toBeGreaterThan(0)
+      const lastChange = changes[changes.length - 1]
+      expect(lastChange.operation.type).toBe('batchUpdateBounds')
+    })
+
+    const lastChange = changes[changes.length - 1]
+    if (lastChange.operation.type === 'batchUpdateBounds') {
+      expect(lastChange.nodeIds).toContain(nodeId)
+      expect(lastChange.operation.bounds[nodeId]?.bounds).toEqual(newBounds)
+    }
+
+    const nodeRef = layoutStore.getNodeLayoutRef(nodeId)
+    expect(nodeRef.value?.position).toEqual({ x: 40, y: 60 })
+    expect(nodeRef.value?.size).toEqual({ width: 220, height: 120 })
+
+    unsubscribe()
+  })
+
   it('should query nodes by spatial bounds', () => {
     const nodes = [
       { id: 'node-a', position: { x: 0, y: 0 } },