diff --git a/packages/vite/src/node/__tests__/shortcuts.spec.ts b/packages/vite/src/node/__tests__/shortcuts.spec.ts
index 90a22f56f8f88d..d2526918551881 100644
--- a/packages/vite/src/node/__tests__/shortcuts.spec.ts
+++ b/packages/vite/src/node/__tests__/shortcuts.spec.ts
@@ -1,3 +1,4 @@
+import type { Mock } from 'vitest'
 import { describe, expect, test, vi } from 'vitest'
 import { createServer } from '../server'
 import { preview } from '../preview'
@@ -26,18 +27,17 @@ describe('bindCLIShortcuts', () => {
       )
 
       expect.assert(
-        server._rl,
+        server._shortcutsState?.rl,
         'The readline interface should be defined after binding shortcuts.',
       )
       expect(xAction).not.toHaveBeenCalled()
 
-      server._rl.emit('line', 'x')
+      server._shortcutsState.rl.emit('line', 'x')
       await vi.waitFor(() => expect(xAction).toHaveBeenCalledOnce())
 
       const xUpdatedAction = vi.fn()
       const zAction = vi.fn()
 
-      xAction.mockClear()
       bindCLIShortcuts(
         server,
         {
@@ -50,18 +50,18 @@ describe('bindCLIShortcuts', () => {
       )
 
       expect(xUpdatedAction).not.toHaveBeenCalled()
-      server._rl.emit('line', 'x')
+      server._shortcutsState.rl.emit('line', 'x')
       await vi.waitFor(() => expect(xUpdatedAction).toHaveBeenCalledOnce())
 
       // Ensure original xAction is not called again
-      expect(xAction).not.toBeCalled()
+      expect(xAction).toHaveBeenCalledOnce()
 
       expect(yAction).not.toHaveBeenCalled()
-      server._rl.emit('line', 'y')
+      server._shortcutsState.rl.emit('line', 'y')
       await vi.waitFor(() => expect(yAction).toHaveBeenCalledOnce())
 
       expect(zAction).not.toHaveBeenCalled()
-      server._rl.emit('line', 'z')
+      server._shortcutsState.rl.emit('line', 'z')
       await vi.waitFor(() => expect(zAction).toHaveBeenCalledOnce())
     } finally {
       await server.close()
@@ -69,45 +69,103 @@ describe('bindCLIShortcuts', () => {
   })
 
   test('rebinds shortcuts after server restart', async () => {
-    const server = await createServer()
+    const manualShortcutAction = vi.fn()
+    const pluginShortcutActions: Array<Mock<any>> = []
+
+    const server = await createServer({
+      plugins: [
+        {
+          name: 'custom-shortcut-plugin',
+          configureServer(viteDevServer) {
+            const action = vi.fn()
+
+            // Keep track of actions created by the plugin
+            // To verify if they are overwritten on server restart
+            pluginShortcutActions.push(action)
+
+            // Bind custom shortcut from plugin
+            bindCLIShortcuts(
+              viteDevServer,
+              {
+                customShortcuts: [
+                  {
+                    key: 'y',
+                    description: 'plugin shortcut',
+                    action,
+                  },
+                ],
+              },
+              true,
+            )
+          },
+        },
+      ],
+    })
 
     try {
-      const action = vi.fn()
+      const readline = server._shortcutsState?.rl
+
+      expect.assert(
+        readline,
+        'The readline interface should be defined after binding shortcuts.',
+      )
+
+      readline.emit('line', 'y')
+      await vi.waitFor(() => {
+        expect(pluginShortcutActions).toHaveLength(1)
+        expect(pluginShortcutActions[0]).toHaveBeenCalledOnce()
+      })
 
+      // Manually bind another custom shortcut
       bindCLIShortcuts(
         server,
         {
-          customShortcuts: [{ key: 'x', description: 'test', action }],
+          customShortcuts: [
+            {
+              key: 'x',
+              description: 'manual shortcut',
+              action: manualShortcutAction,
+            },
+          ],
         },
         true,
       )
 
-      // Verify shortcut works initially
-      const initialReadline = server._rl
-
-      expect.assert(
-        initialReadline,
-        'The readline interface should be defined after binding shortcuts.',
+      readline.emit('line', 'x')
+      await vi.waitFor(() =>
+        expect(manualShortcutAction).toHaveBeenCalledOnce(),
       )
 
-      initialReadline.emit('line', 'x')
-
-      await vi.waitFor(() => expect(action).toHaveBeenCalledOnce())
+      // Check the order of shortcuts before restart
+      expect(
+        server._shortcutsState?.options.customShortcuts?.map((s) => s.key),
+      ).toEqual(['x', 'y'])
 
       // Restart the server
-      action.mockClear()
       await server.restart()
 
-      const newReadline = server._rl
+      // Shortcut orders should be preserved after restart
+      expect(
+        server._shortcutsState?.options.customShortcuts?.map((s) => s.key),
+      ).toEqual(['x', 'y'])
 
       expect.assert(
-        newReadline && newReadline !== initialReadline,
-        'A new readline interface should be created after server restart.',
+        server._shortcutsState?.rl === readline,
+        'The readline interface should be preserved.',
       )
 
       // Shortcuts should still work after restart
-      newReadline.emit('line', 'x')
-      await vi.waitFor(() => expect(action).toHaveBeenCalledOnce())
+      readline.emit('line', 'x')
+      await vi.waitFor(() =>
+        expect(manualShortcutAction).toHaveBeenCalledTimes(2),
+      )
+
+      readline.emit('line', 'y')
+      await vi.waitFor(() => {
+        expect(pluginShortcutActions).toHaveLength(2)
+        expect(pluginShortcutActions[1]).toHaveBeenCalledOnce()
+        expect(pluginShortcutActions[0]).toHaveBeenCalledOnce()
+      })
     } finally {
       await server.close()
     }
diff --git a/packages/vite/src/node/preview.ts b/packages/vite/src/node/preview.ts
index 6fc8e914fd69fd..f4db13030c24c1 100644
--- a/packages/vite/src/node/preview.ts
+++ b/packages/vite/src/node/preview.ts
@@ -1,6 +1,5 @@
 import fs from 'node:fs'
 import path from 'node:path'
-import type readline from 'node:readline'
 import sirv from 'sirv'
 import compression from '@polka/compression'
 import connect from 'connect'
@@ -36,7 +35,7 @@ import {
 } from './utils'
 import { printServerUrls } from './logger'
 import { bindCLIShortcuts } from './shortcuts'
-import type { BindCLIShortcutsOptions } from './shortcuts'
+import type { BindCLIShortcutsOptions, ShortcutsState } from './shortcuts'
 import { resolveConfig } from './config'
 import type { InlineConfig, ResolvedConfig } from './config'
 import { DEFAULT_PREVIEW_PORT } from './constants'
@@ -113,11 +112,7 @@ export interface PreviewServer {
   /**
    * @internal
    */
-  _shortcutsOptions?: BindCLIShortcutsOptions<PreviewServer>
-  /**
-   * @internal
-   */
-  _rl?: readline.Interface | undefined
+  _shortcutsState?: ShortcutsState<PreviewServer>
 }
 
 export type PreviewServerHook = (
diff --git a/packages/vite/src/node/server/index.ts b/packages/vite/src/node/server/index.ts
index 06a8ff27773cd0..cf75ea0c6cd2ab 100644
--- a/packages/vite/src/node/server/index.ts
+++ b/packages/vite/src/node/server/index.ts
@@ -6,7 +6,6 @@ import { get as httpsGet } from 'node:https'
 import type * as http from 'node:http'
 import { performance } from 'node:perf_hooks'
 import type { Http2SecureServer } from 'node:http2'
-import type readline from 'node:readline'
 import connect from 'connect'
 import corsMiddleware from 'cors'
 import colors from 'picocolors'
@@ -46,7 +45,7 @@ import { ssrFixStacktrace, ssrRewriteStacktrace } from '../ssr/ssrStacktrace'
 import { ssrTransform } from '../ssr/ssrTransform'
 import { reloadOnTsconfigChange } from '../plugins/esbuild'
 import { bindCLIShortcuts } from '../shortcuts'
-import type { BindCLIShortcutsOptions } from '../shortcuts'
+import type { BindCLIShortcutsOptions, ShortcutsState } from '../shortcuts'
 import {
   CLIENT_DIR,
   DEFAULT_DEV_PORT,
@@ -407,11 +406,7 @@ export interface ViteDevServer {
   /**
    * @internal
    */
-  _shortcutsOptions?: BindCLIShortcutsOptions<ViteDevServer>
-  /**
-   * @internal
-   */
-  _rl?: readline.Interface | undefined
+  _shortcutsState?: ShortcutsState<ViteDevServer>
   /**
    * @internal
    */
@@ -442,6 +437,7 @@ export async function _createServer(
   options: {
     listen: boolean
     previousEnvironments?: Record<string, DevEnvironment>
+    previousShortcutsState?: ShortcutsState<ViteDevServer>
   },
 ): Promise<ViteDevServer> {
   const config = isResolvedConfig(inlineConfig)
@@ -773,7 +769,7 @@ export async function _createServer(
     },
     _restartPromise: null,
     _forceOptimizeOnRestart: false,
-    _shortcutsOptions: undefined,
+    _shortcutsState: options.previousShortcutsState,
   }
 
   // maintain consistency with the server instance after restarting.
@@ -1215,7 +1211,6 @@ export function resolveServerOptions(
 
 async function restartServer(server: ViteDevServer) {
   global.__vite_start_time = performance.now()
-  const shortcutsOptions = server._shortcutsOptions
 
   let inlineConfig = server.config.inlineConfig
   if (server._forceOptimizeOnRestart) {
@@ -1236,6 +1231,7 @@ async function restartServer(server: ViteDevServer) {
       newServer = await _createServer(inlineConfig, {
         listen: false,
         previousEnvironments: server.environments,
+        previousShortcutsState: server._shortcutsState,
       })
     } catch (err: any) {
       server.config.logger.error(err.message, {
@@ -1245,14 +1241,15 @@ async function restartServer(server: ViteDevServer) {
       return
     }
 
+    // Detach readline so close handler skips it. Reused to avoid stdin issues
+    server._shortcutsState = undefined
+
     await server.close()
 
     // Assign new server props to existing server instance
     const middlewares = server.middlewares
     newServer._configServerPort = server._configServerPort
     newServer._currentServerPort = server._currentServerPort
-    // Ensure the new server has no stale readline reference
-    newServer._rl = undefined
     Object.assign(server, newServer)
 
     // Keep the same connect instance so app.use(vite.middlewares) works
@@ -1277,11 +1274,13 @@ async function restartServer(server: ViteDevServer) {
   }
   logger.info('server restarted.', { timestamp: true })
 
-  if (shortcutsOptions) {
-    shortcutsOptions.print = false
+  if (
+    (server._shortcutsState as ShortcutsState<ViteDevServer> | undefined)
+      ?.options
+  ) {
     bindCLIShortcuts(
       server,
-      shortcutsOptions,
+      { print: false },
       // Skip environment checks since shortcuts were bound before restart
       true,
     )
diff --git a/packages/vite/src/node/shortcuts.ts b/packages/vite/src/node/shortcuts.ts
index bbca13dd58a27a..4583099f4f421c 100644
--- a/packages/vite/src/node/shortcuts.ts
+++ b/packages/vite/src/node/shortcuts.ts
@@ -6,6 +6,11 @@ import { isDevServer } from './utils'
 import type { PreviewServer } from './preview'
 import { openBrowser } from './server/openBrowser'
 
+export type ShortcutsState<Server = ViteDevServer | PreviewServer> = {
+  rl: readline.Interface
+  options: BindCLIShortcutsOptions<Server>
+}
+
 export type BindCLIShortcutsOptions<Server = ViteDevServer | PreviewServer> = {
   /**
    * Print a one-line shortcuts "help" hint to the terminal
@@ -36,18 +41,19 @@ export function bindCLIShortcuts<Server extends ViteDevServer | PreviewServer>(
 
   const isDev = isDevServer(server)
 
-  const customShortcuts: CLIShortcut<ViteDevServer | PreviewServer>[] =
-    opts?.customShortcuts ?? []
-
-  // Merge custom shortcuts from existing options
-  // with new shortcuts taking priority
-  for (const shortcut of server._shortcutsOptions?.customShortcuts ?? []) {
-    if (!customShortcuts.some((s) => s.key === shortcut.key)) {
-      customShortcuts.push(shortcut)
-    }
-  }
-
-  server._shortcutsOptions = {
+  // Merge shortcuts: new at top, existing updated in place (keeps manual > plugin order)
+  const previousShortcuts =
+    server._shortcutsState?.options.customShortcuts ?? []
+  const newShortcuts = opts?.customShortcuts ?? []
+  const previousKeys = new Set(previousShortcuts.map((s) => s.key))
+  const customShortcuts: CLIShortcut<ViteDevServer | PreviewServer>[] = [
+    ...newShortcuts.filter((s) => !previousKeys.has(s.key)),
+    ...previousShortcuts.map(
+      (s) => newShortcuts.find((n) => n.key === s.key) ?? s,
+    ),
+  ]
+
+  const newOptions: BindCLIShortcutsOptions<Server> = {
     ...opts,
     customShortcuts,
   }
@@ -100,15 +106,22 @@ export function bindCLIShortcuts<Server extends ViteDevServer | PreviewServer>(
     actionRunning = false
   }
 
-  if (!server._rl) {
-    const rl = readline.createInterface({ input: process.stdin })
-    server._rl = rl
-    server.httpServer.on('close', () => rl.close())
+  if (!server._shortcutsState) {
+    ;(server._shortcutsState as unknown as ShortcutsState<Server>) = {
+      rl: readline.createInterface({ input: process.stdin }),
+      options: newOptions,
+    }
+    server.httpServer.on('close', () => {
+      // Skip if detached during restart (readline is reused)
+      if (server._shortcutsState) server._shortcutsState.rl.close()
+    })
   } else {
-    server._rl.removeAllListeners('line')
+    server._shortcutsState.rl.removeAllListeners('line')
+    ;(server._shortcutsState.options as BindCLIShortcutsOptions<Server>) =
+      newOptions
   }
 
-  server._rl.on('line', onInput)
+  server._shortcutsState!.rl.on('line', onInput)
 }
 
 const BASE_DEV_SHORTCUTS: CLIShortcut<ViteDevServer>[] = [