diff --git a/packages/vite/src/node/__tests__/config.spec.ts b/packages/vite/src/node/__tests__/config.spec.ts
index 6ccbe75f421c27..85737eafe3f8fb 100644
--- a/packages/vite/src/node/__tests__/config.spec.ts
+++ b/packages/vite/src/node/__tests__/config.spec.ts
@@ -6,7 +6,7 @@ import type { InlineConfig, PluginOption } from '..'
 import type { UserConfig, UserConfigExport } from '../config'
 import { defineConfig, loadConfigFromFile, resolveConfig } from '../config'
 import { resolveEnvPrefix } from '../env'
-import { mergeConfig } from '../utils'
+import { hasBothRollupOptionsAndRolldownOptions, mergeConfig } from '../utils'
 import { createLogger } from '../logger'
 
 describe('mergeConfig', () => {
@@ -560,6 +560,46 @@ describe('mergeConfig', () => {
     expect(downOutput.hashCharacters).toBe('base36')
   })
 
+  test('hasBothRollupOptionsAndRolldownOptions returns false when only rollupOptions is set', () => {
+    // When mergeConfig is called with only rollupOptions in the override,
+    // setupRollupOptionCompat creates a proxy where rollupOptions === rolldownOptions.
+    // hasBothRollupOptionsAndRolldownOptions should return false in this case
+    // to avoid false positive warnings.
+    const baseConfig = defineConfig({
+      build: {}, // Need existing build object for recursive merge to happen
+    })
+    const newConfig = defineConfig({
+      build: {
+        rollupOptions: {
+          treeshake: false,
+        },
+      },
+    })
+    const mergedConfig: UserConfig = mergeConfig(baseConfig, newConfig)
+
+    expect(mergedConfig.build!.rollupOptions).toBeDefined()
+    expect(mergedConfig.build!.rolldownOptions).toBeDefined()
+    expect(mergedConfig.build!.rollupOptions).toBe(
+      mergedConfig.build!.rolldownOptions,
+    )
+
+    expect(hasBothRollupOptionsAndRolldownOptions(mergedConfig)).toBe(false)
+  })
+
+  test('hasBothRollupOptionsAndRolldownOptions returns true when both are explicitly set to different values', () => {
+    const config = defineConfig({
+      build: {
+        rollupOptions: {
+          treeshake: false,
+        },
+        rolldownOptions: {
+          platform: 'neutral',
+        },
+      },
+    })
+    expect(hasBothRollupOptionsAndRolldownOptions(config)).toBe(true)
+  })
+
   test('rollupOptions/rolldownOptions.platform', async () => {
     const testRollupOptions = await resolveConfig(
       {
diff --git a/packages/vite/src/node/utils.ts b/packages/vite/src/node/utils.ts
index 52ba8b067c1609..8576b8e2b05261 100644
--- a/packages/vite/src/node/utils.ts
+++ b/packages/vite/src/node/utils.ts
@@ -1317,7 +1317,9 @@ export function hasBothRollupOptionsAndRolldownOptions(
     if (
       opt != null &&
       opt.rollupOptions != null &&
-      opt.rolldownOptions != null
+      opt.rolldownOptions != null &&
+      // Check they are not just proxy values created by setupRollupOptionCompat
+      opt.rollupOptions !== opt.rolldownOptions
     ) {
       return true
     }