diff --git a/src/api-extractor.ts b/src/api-extractor.ts
index ea2a5a6c..8e269e9e 100644
--- a/src/api-extractor.ts
+++ b/src/api-extractor.ts
@@ -17,6 +17,7 @@ import {
   defaultOutExtension,
   ensureTempDeclarationDir,
   getApiExtractor,
+  removeFiles,
   toAbsolutePath,
   writeFileSync,
 } from './utils'
@@ -135,6 +136,12 @@ async function rollupDtsFiles(
   }
 }
 
+function cleanDtsFiles(options: NormalizedOptions) {
+  if (options.clean) {
+    removeFiles(['**/*.d.{ts,mts,cts}'], options.outDir)
+  }
+}
+
 export async function runDtsRollup(
   options: NormalizedOptions,
   exports?: ExportDeclaration[]
@@ -149,6 +156,7 @@ export async function runDtsRollup(
     if (!exports) {
       throw new Error('Unexpected internal error: dts exports is not define')
     }
+    cleanDtsFiles(options)
     for (const format of options.format) {
       await rollupDtsFiles(options, exports, format)
     }
diff --git a/test/index.test.ts b/test/index.test.ts
index 7d47613b..71c946a2 100644
--- a/test/index.test.ts
+++ b/test/index.test.ts
@@ -1669,24 +1669,49 @@ test('should only include exported declarations with experimentalDts', async ()
   expect(entry2dts).not.toContain('declare1')
 })
 
-test('--experimental-dts should work when --clean is provided', async () => {
-  const files = {
+test('.d.ts files should be cleaned when --clean and --experimental-dts are provided', async () => {
+  const filesFoo = {
     'package.json': `{ "name": "tsup-playground", "private": true }`,
-    'input.ts': `export const foo = 1`,
+    'foo.ts': `export const foo = 1`,
+  }
+
+  const filesFooBar = {
+    ...filesFoo,
+    'bar.ts': `export const bar = 2`,
   }
-  const withoutClean = await run(getTestName(), files, {
+
+  // First run with both foo and bar
+  const result1 = await run(getTestName(), filesFooBar, {
+    entry: ['foo.ts', 'bar.ts'],
+    flags: ['--experimental-dts'],
+  })
+
+  expect(result1.outFiles).toContain('foo.d.ts')
+  expect(result1.outFiles).toContain('foo.js')
+  expect(result1.outFiles).toContain('bar.d.ts')
+  expect(result1.outFiles).toContain('bar.js')
+
+  // Second run with only foo
+  const result2 = await run(getTestName(), filesFoo, {
+    entry: ['foo.ts'],
     flags: ['--experimental-dts'],
   })
-  const withClean = await run(getTestName(), files, {
+
+  // When --clean is not provided, the previous bar.* files should still exist
+  expect(result2.outFiles).toContain('foo.d.ts')
+  expect(result2.outFiles).toContain('foo.js')
+  expect(result2.outFiles).toContain('bar.d.ts')
+  expect(result2.outFiles).toContain('bar.js')
+
+  // Third run with only foo and --clean
+  const result3 = await run(getTestName(), filesFoo, {
+    entry: ['foo.ts'],
     flags: ['--experimental-dts', '--clean'],
   })
 
-  expect(withClean.outFiles).toEqual(withoutClean.outFiles)
-  expect(withClean.outFiles).toMatchInlineSnapshot(`
-    [
-      "_tsup-dts-rollup.d.ts",
-      "input.d.ts",
-      "input.js",
-    ]
-  `)
+  // When --clean is provided, the previous bar.* files should be deleted
+  expect(result3.outFiles).toContain('foo.d.ts')
+  expect(result3.outFiles).toContain('foo.js')
+  expect(result3.outFiles).not.toContain('bar.d.ts')
+  expect(result3.outFiles).not.toContain('bar.js')
 })