diff --git a/src/lib/litegraph/src/LGraphCanvas.ts b/src/lib/litegraph/src/LGraphCanvas.ts
index ebd4d2c69..4dde55cb4 100644
--- a/src/lib/litegraph/src/LGraphCanvas.ts
+++ b/src/lib/litegraph/src/LGraphCanvas.ts
@@ -5639,6 +5639,12 @@ export class LGraphCanvas implements CustomEventDispatcher<LGraphCanvasEventMap>
     this.renderedPaths.clear()
     if (this.links_render_mode === LinkRenderType.HIDDEN_LINK) return
 
+    // Skip link rendering while waiting for slot positions to sync after reconfigure
+    if (LiteGraph.vueNodesMode && layoutStore.pendingSlotSync) {
+      this.#visibleReroutes.clear()
+      return
+    }
+
     const { graph, subgraph } = this
     if (!graph) throw new NullGraphError()
 
diff --git a/src/renderer/core/layout/store/layoutStore.ts b/src/renderer/core/layout/store/layoutStore.ts
index 786be0625..ed928bb00 100644
--- a/src/renderer/core/layout/store/layoutStore.ts
+++ b/src/renderer/core/layout/store/layoutStore.ts
@@ -141,6 +141,20 @@ class LayoutStoreImpl implements LayoutStore {
   // Vue resizing state to prevent drag from activating during resize
   public isResizingVueNodes = ref(false)
 
+  /**
+   * Flag indicating slot positions are pending sync after graph reconfiguration.
+   * When true, link rendering should be skipped to avoid drawing with stale positions.
+   */
+  private _pendingSlotSync = false
+
+  get pendingSlotSync(): boolean {
+    return this._pendingSlotSync
+  }
+
+  setPendingSlotSync(value: boolean): void {
+    this._pendingSlotSync = value
+  }
+
   constructor() {
     // Initialize Yjs data structures
     this.ynodes = this.ydoc.getMap('nodes')
diff --git a/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts b/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts
index 8cedc8200..1f8ca29a9 100644
--- a/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts
+++ b/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts
@@ -12,6 +12,7 @@ import { useSharedCanvasPositionConversion } from '@/composables/element/useCanv
 import { LiteGraph } from '@/lib/litegraph/src/litegraph'
 import { getSlotKey } from '@/renderer/core/layout/slots/slotIdentifier'
 import { layoutStore } from '@/renderer/core/layout/store/layoutStore'
+import { app } from '@/scripts/app'
 import type { SlotLayout } from '@/renderer/core/layout/types'
 import {
   isPointEqual,
@@ -28,16 +29,36 @@ const raf = createRafBatch(() => {
 
 function scheduleSlotLayoutSync(nodeId: string) {
   pendingNodes.add(nodeId)
+  // Re-assert pending flag for late mounts (Vue components mounting after
+  // flushScheduledSlotLayoutSync was called synchronously in onConfigure)
+  layoutStore.setPendingSlotSync(true)
   raf.schedule()
 }
 
-function flushScheduledSlotLayoutSync() {
-  if (pendingNodes.size === 0) return
+export function flushScheduledSlotLayoutSync() {
+  if (pendingNodes.size === 0) {
+    // No pending nodes - check if we should wait for Vue components to mount
+    const graph = app.canvas?.graph
+    const hasNodes = graph && graph._nodes && graph._nodes.length > 0
+    if (hasNodes) {
+      // Graph has nodes but Vue hasn't mounted them yet - keep flag set
+      // so late mounts can re-assert it via scheduleSlotLayoutSync()
+      return
+    }
+    // No nodes in graph - safe to clear the flag (no Vue components will mount)
+    layoutStore.setPendingSlotSync(false)
+    app.canvas?.setDirty(true, true)
+    return
+  }
   const conv = useSharedCanvasPositionConversion()
   for (const nodeId of Array.from(pendingNodes)) {
     pendingNodes.delete(nodeId)
     syncNodeSlotLayoutsFromDOM(nodeId, conv)
   }
+  // Clear the pending sync flag - slots are now synced
+  layoutStore.setPendingSlotSync(false)
+  // Trigger canvas redraw now that links can render with correct positions
+  app.canvas?.setDirty(true, true)
 }
 
 export function syncNodeSlotLayoutsFromDOM(
diff --git a/src/scripts/app.ts b/src/scripts/app.ts
index f838d7906..f89566403 100644
--- a/src/scripts/app.ts
+++ b/src/scripts/app.ts
@@ -5,6 +5,8 @@ import { reactive, unref } from 'vue'
 import { shallowRef } from 'vue'
 
 import { useCanvasPositionConversion } from '@/composables/element/useCanvasPositionConversion'
+import { layoutStore } from '@/renderer/core/layout/store/layoutStore'
+import { flushScheduledSlotLayoutSync } from '@/renderer/extensions/vueNodes/composables/useSlotElementTracking'
 import { registerProxyWidgets } from '@/core/graph/subgraph/proxyWidget'
 import { st, t } from '@/i18n'
 import type { IContextMenuValue } from '@/lib/litegraph/src/interfaces'
@@ -734,17 +736,31 @@ export class ComfyApp {
   private addAfterConfigureHandler(graph: LGraph) {
     const { onConfigure } = graph
     graph.onConfigure = function (...args) {
-      fixLinkInputSlots(this)
+      // Set pending sync flag to suppress link rendering until slots are synced
+      if (LiteGraph.vueNodesMode) {
+        layoutStore.setPendingSlotSync(true)
+      }
 
-      // Fire callbacks before the onConfigure, this is used by widget inputs to setup the config
-      triggerCallbackOnAllNodes(this, 'onGraphConfigured')
+      try {
+        fixLinkInputSlots(this)
 
-      const r = onConfigure?.apply(this, args)
+        // Fire callbacks before the onConfigure, this is used by widget inputs to setup the config
+        triggerCallbackOnAllNodes(this, 'onGraphConfigured')
 
-      // Fire after onConfigure, used by primitives to generate widget using input nodes config
-      triggerCallbackOnAllNodes(this, 'onAfterGraphConfigured')
+        const r = onConfigure?.apply(this, args)
 
-      return r
+        // Fire after onConfigure, used by primitives to generate widget using input nodes config
+        triggerCallbackOnAllNodes(this, 'onAfterGraphConfigured')
+
+        return r
+      } finally {
+        // Flush pending slot layout syncs to fix link alignment after undo/redo
+        // Using finally ensures links aren't permanently suppressed if an error occurs
+        if (LiteGraph.vueNodesMode) {
+          flushScheduledSlotLayoutSync()
+          app.canvas?.setDirty(true, true)
+        }
+      }
     }
   }