diff --git a/src/components/dialog/content/setting/KeybindingPanel.test.ts b/src/components/dialog/content/setting/KeybindingPanel.test.ts
new file mode 100644
index 0000000000..948faaf502
--- /dev/null
+++ b/src/components/dialog/content/setting/KeybindingPanel.test.ts
@@ -0,0 +1,252 @@
+import { mount } from '@vue/test-utils'
+import { createPinia, setActivePinia } from 'pinia'
+import PrimeVue from 'primevue/config'
+import Tooltip from 'primevue/tooltip'
+import { beforeEach, describe, expect, it, vi } from 'vitest'
+import { nextTick } from 'vue'
+import { createI18n } from 'vue-i18n'
+
+import KeybindingPanel from './KeybindingPanel.vue'
+import {
+  KeyComboImpl,
+  KeybindingImpl,
+  useKeybindingStore
+} from '@/stores/keybindingStore'
+
+const i18n = createI18n({
+  legacy: false,
+  locale: 'en',
+  messages: { en: {} }
+})
+
+const mockPersist = vi.fn().mockResolvedValue(undefined)
+vi.mock('@/services/keybindingService', () => ({
+  useKeybindingService: () => ({
+    persistUserKeybindings: mockPersist
+  })
+}))
+
+vi.mock('primevue/usetoast', () => ({
+  useToast: () => ({
+    add: vi.fn()
+  })
+}))
+
+vi.mock('@/stores/commandStore', () => ({
+  useCommandStore: () => ({
+    commands: {
+      'test-command': { id: 'test-command', label: 'Test Command' },
+      'command-a': { id: 'command-a', label: 'Command A' },
+      'command-b': { id: 'command-b', label: 'Command B' }
+    }
+  })
+}))
+
+describe('KeybindingPanel', () => {
+  beforeEach(() => {
+    setActivePinia(createPinia())
+    vi.clearAllMocks()
+  })
+
+  const mountPanel = () => {
+    return mount(KeybindingPanel, {
+      global: {
+        plugins: [PrimeVue, i18n],
+        directives: { tooltip: Tooltip },
+        stubs: {
+          DataTable: true,
+          Column: true,
+          Dialog: {
+            template:
+              '<div v-if="visible"><slot /><slot name="footer" /></div>',
+            props: ['visible', 'header']
+          },
+          InputText: true,
+          Message: true,
+          Tag: true,
+          Button: true,
+          SearchBox: true,
+          PanelTemplate: {
+            template: '<div><slot /><slot name="header" /></div>'
+          },
+          KeyComboDisplay: true
+        }
+      }
+    })
+  }
+
+  describe('saveKeybinding', () => {
+    it('should close dialog before updating store to prevent warning flash', async () => {
+      const keybindingStore = useKeybindingStore()
+      let dialogVisibleWhenStoreUpdated: boolean | undefined
+
+      const wrapper = mountPanel()
+      const vm = wrapper.vm as InstanceType<typeof KeybindingPanel>
+
+      // Patch keybindingStore to capture dialog state when store is updated
+      const originalUpdate = keybindingStore.updateKeybindingOnCommand
+      keybindingStore.updateKeybindingOnCommand = (keybinding) => {
+        dialogVisibleWhenStoreUpdated = (
+          vm as unknown as { editDialogVisible: boolean }
+        ).editDialogVisible
+        return originalUpdate.call(keybindingStore, keybinding)
+      }
+
+      // Setup editing state
+      ;(
+        vm as unknown as { currentEditingCommand: { id: string } }
+      ).currentEditingCommand = { id: 'test-command' }
+      ;(
+        vm as unknown as { newBindingKeyCombo: KeyComboImpl }
+      ).newBindingKeyCombo = new KeyComboImpl({ key: 's', ctrl: true })
+      ;(vm as unknown as { editDialogVisible: boolean }).editDialogVisible =
+        true
+
+      await (
+        vm as unknown as { saveKeybinding: () => Promise<void> }
+      ).saveKeybinding()
+
+      // Dialog should be closed when store updates (prevents warning flash)
+      expect(dialogVisibleWhenStoreUpdated).toBe(false)
+    })
+
+    it('should persist keybinding after closing dialog', async () => {
+      const wrapper = mountPanel()
+      const vm = wrapper.vm as InstanceType<typeof KeybindingPanel>
+
+      // Setup editing state
+      ;(
+        vm as unknown as { currentEditingCommand: { id: string } }
+      ).currentEditingCommand = { id: 'test-command' }
+      ;(
+        vm as unknown as { newBindingKeyCombo: KeyComboImpl }
+      ).newBindingKeyCombo = new KeyComboImpl({ key: 's', ctrl: true })
+      ;(vm as unknown as { editDialogVisible: boolean }).editDialogVisible =
+        true
+
+      await (
+        vm as unknown as { saveKeybinding: () => Promise<void> }
+      ).saveKeybinding()
+
+      expect(mockPersist).toHaveBeenCalled()
+      expect(
+        (vm as unknown as { editDialogVisible: boolean }).editDialogVisible
+      ).toBe(false)
+    })
+
+    it('should not show warning after save button is clicked', async () => {
+      const keybindingStore = useKeybindingStore()
+
+      // Setup existing keybinding that will conflict
+      keybindingStore.addUserKeybinding(
+        new KeybindingImpl({
+          commandId: 'existing-command',
+          combo: new KeyComboImpl({ key: 's', ctrl: true })
+        })
+      )
+
+      const wrapper = mountPanel()
+      const vm = wrapper.vm as InstanceType<typeof KeybindingPanel>
+
+      // Setup editing with conflicting combo
+      ;(
+        vm as unknown as {
+          currentEditingCommand: { id: string; keybinding: null }
+        }
+      ).currentEditingCommand = {
+        id: 'new-command',
+        keybinding: null
+      }
+      ;(
+        vm as unknown as { newBindingKeyCombo: KeyComboImpl }
+      ).newBindingKeyCombo = new KeyComboImpl({ key: 's', ctrl: true })
+      ;(vm as unknown as { editDialogVisible: boolean }).editDialogVisible =
+        true
+      await nextTick()
+
+      // Verify warning is shown before save
+      expect(
+        (vm as unknown as { existingKeybindingOnCombo: KeybindingImpl | null })
+          .existingKeybindingOnCombo
+      ).not.toBeNull()
+
+      // Click save
+      await (
+        vm as unknown as { saveKeybinding: () => Promise<void> }
+      ).saveKeybinding()
+      await nextTick()
+
+      // After save, dialog should be closed AND state should be cleared
+      expect(
+        (vm as unknown as { editDialogVisible: boolean }).editDialogVisible
+      ).toBe(false)
+      expect(
+        (vm as unknown as { currentEditingCommand: null }).currentEditingCommand
+      ).toBeNull()
+      expect(
+        (vm as unknown as { newBindingKeyCombo: null }).newBindingKeyCombo
+      ).toBeNull()
+    })
+  })
+
+  describe('keybinding overwrite flow', () => {
+    it('should successfully overwrite existing keybinding without flash', async () => {
+      const keybindingStore = useKeybindingStore()
+
+      // Setup existing keybinding
+      keybindingStore.addUserKeybinding(
+        new KeybindingImpl({
+          commandId: 'command-a',
+          combo: new KeyComboImpl({ key: 'a', ctrl: true })
+        })
+      )
+
+      const wrapper = mountPanel()
+      const vm = wrapper.vm as InstanceType<typeof KeybindingPanel>
+
+      // Open edit for command-b with same combo (conflict)
+      ;(
+        vm as unknown as {
+          currentEditingCommand: { id: string; keybinding: null }
+        }
+      ).currentEditingCommand = {
+        id: 'command-b',
+        keybinding: null
+      }
+      ;(
+        vm as unknown as { newBindingKeyCombo: KeyComboImpl }
+      ).newBindingKeyCombo = new KeyComboImpl({ key: 'a', ctrl: true })
+      ;(vm as unknown as { editDialogVisible: boolean }).editDialogVisible =
+        true
+      await nextTick()
+
+      // Verify conflict detected
+      expect(
+        (vm as unknown as { existingKeybindingOnCombo: KeybindingImpl })
+          .existingKeybindingOnCombo?.commandId
+      ).toBe('command-a')
+
+      // Save (overwrite)
+      await (
+        vm as unknown as { saveKeybinding: () => Promise<void> }
+      ).saveKeybinding()
+
+      // Verify dialog closed
+      expect(
+        (vm as unknown as { editDialogVisible: boolean }).editDialogVisible
+      ).toBe(false)
+
+      // Verify new keybinding saved
+      expect(
+        keybindingStore.getKeybindingByCommandId('command-b')
+      ).toBeDefined()
+
+      // Verify combo now belongs to command-b
+      const combo = new KeyComboImpl({ key: 'a', ctrl: true })
+      expect(keybindingStore.getKeybinding(combo)?.commandId).toBe('command-b')
+
+      // Verify persistence called
+      expect(mockPersist).toHaveBeenCalled()
+    })
+  })
+})
diff --git a/src/components/dialog/content/setting/KeybindingPanel.vue b/src/components/dialog/content/setting/KeybindingPanel.vue
index 03ca3df47c..4e4b141e72 100644
--- a/src/components/dialog/content/setting/KeybindingPanel.vue
+++ b/src/components/dialog/content/setting/KeybindingPanel.vue
@@ -145,7 +145,7 @@ import InputText from 'primevue/inputtext'
 import Message from 'primevue/message'
 import Tag from 'primevue/tag'
 import { useToast } from 'primevue/usetoast'
-import { computed, ref, watchEffect } from 'vue'
+import { computed, ref, watch } from 'vue'
 import { useI18n } from 'vue-i18n'
 
 import SearchBox from '@/components/common/SearchBox.vue'
@@ -194,7 +194,7 @@ const selectedCommandData = ref<ICommandData | null>(null)
 const editDialogVisible = ref(false)
 const newBindingKeyCombo = ref<KeyComboImpl | null>(null)
 const currentEditingCommand = ref<ICommandData | null>(null)
-const keybindingInput = ref<InstanceType<typeof InputText> | null>(null)
+const keybindingInput = ref()
 
 const existingKeybindingOnCombo = computed<KeybindingImpl | null>(() => {
   if (!currentEditingCommand.value) {
@@ -225,11 +225,9 @@ function editKeybinding(commandData: ICommandData) {
   editDialogVisible.value = true
 }
 
-watchEffect(() => {
-  if (editDialogVisible.value) {
-    // nextTick doesn't work here, so we use a timeout instead
+watch(editDialogVisible, (visible) => {
+  if (visible) {
     setTimeout(() => {
-      // @ts-expect-error - $el is an internal property of the InputText component
       keybindingInput.value?.$el?.focus()
     }, 300)
   }
@@ -265,18 +263,23 @@ function cancelEdit() {
 }
 
 async function saveKeybinding() {
-  if (currentEditingCommand.value && newBindingKeyCombo.value) {
-    const updated = keybindingStore.updateKeybindingOnCommand(
-      new KeybindingImpl({
-        commandId: currentEditingCommand.value.id,
-        combo: newBindingKeyCombo.value
-      })
-    )
-    if (updated) {
-      await keybindingService.persistUserKeybindings()
-    }
-  }
+  if (!currentEditingCommand.value || !newBindingKeyCombo.value) return
+
+  // Capture values before closing dialog
+  const commandId = currentEditingCommand.value.id
+  const combo = newBindingKeyCombo.value
+
+  // Close dialog FIRST to prevent warning flash during store update
   cancelEdit()
+
+  // Update store after dialog is closed
+  const updated = keybindingStore.updateKeybindingOnCommand(
+    new KeybindingImpl({ commandId, combo })
+  )
+
+  if (updated) {
+    await keybindingService.persistUserKeybindings()
+  }
 }
 
 async function resetKeybinding(commandData: ICommandData) {