diff --git a/src/features/clean.test.ts b/src/features/clean.test.ts
new file mode 100644
index 000000000..badc04aa0
--- /dev/null
+++ b/src/features/clean.test.ts
@@ -0,0 +1,97 @@
+import fs from 'node:fs'
+import { mkdir, mkdtemp, writeFile } from 'node:fs/promises'
+import { syncBuiltinESMExports } from 'node:module'
+import { tmpdir } from 'node:os'
+import path from 'node:path'
+import { afterEach, beforeEach, describe, expect, test, vi } from 'vitest'
+import { fsExists, fsRemove } from '../utils/fs.ts'
+import { cleanOutDir, resolveClean } from './clean.ts'
+import type { ResolvedConfig, UserConfig } from '../config/index.ts'
+
+let cwd: string
+
+beforeEach(async () => {
+  cwd = await mkdtemp(path.join(tmpdir(), 'tsdown-clean-'))
+})
+
+afterEach(async () => {
+  vi.restoreAllMocks()
+  syncBuiltinESMExports()
+  await fsRemove(cwd)
+})
+
+async function writeFiles(files: string[]) {
+  for (const file of files) {
+    const filePath = path.join(cwd, file)
+    await mkdir(path.dirname(filePath), { recursive: true })
+    await writeFile(filePath, '')
+  }
+}
+
+async function clean(outDir: string, clean: UserConfig['clean']) {
+  const resolvedOutDir = path.resolve(cwd, outDir)
+  const config: Partial<ResolvedConfig> = {
+    cwd,
+    outDir: resolvedOutDir,
+    clean: resolveClean(clean, resolvedOutDir, cwd),
+  }
+  // Patch the CommonJS module and sync the ESM bindings so the spy sees the
+  // directory reads made inside tinyglobby
+  const readdir = vi.spyOn(fs, 'readdir')
+  syncBuiltinESMExports()
+  await cleanOutDir([config as ResolvedConfig])
+  return readdir.mock.calls.map(([dir]) =>
+    path.relative(cwd, String(dir)).replaceAll('\\', '/'),
+  )
+}
+
+describe('cleanOutDir', () => {
+  test('lists only the default output directory', async () => {
+    await writeFiles(['dist/old.js', 'dist/nested/old.js', 'sibling.txt'])
+
+    const listed = await clean('dist', true)
+
+    expect(listed.toSorted()).toEqual(['dist', 'dist/nested'])
+    expect(await fsExists(path.join(cwd, 'dist'))).toBe(true)
+    expect(await fsExists(path.join(cwd, 'dist/old.js'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'dist/nested'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'sibling.txt'))).toBe(true)
+  })
+
+  test('lists only a nested custom output directory', async () => {
+    await writeFiles(['out/lib/old.js', 'out/other.js'])
+
+    const listed = await clean('out/lib', true)
+
+    expect(listed).toEqual(['out/lib'])
+    expect(await fsExists(path.join(cwd, 'out/lib/old.js'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'out/other.js'))).toBe(true)
+  })
+
+  test('does not list anything outside a missing output directory', async () => {
+    const listed = await clean('dist', true)
+
+    expect(listed).toEqual(['dist'])
+  })
+
+  test('still removes other custom patterns', async () => {
+    await writeFiles(['dist/old.js', 'temp/old.js', 'app.log', 'keep.js'])
+
+    await clean('dist', ['dist', 'temp', '*.log'])
+
+    expect(await fsExists(path.join(cwd, 'dist'))).toBe(true)
+    expect(await fsExists(path.join(cwd, 'dist/old.js'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'temp'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'app.log'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'keep.js'))).toBe(true)
+  })
+
+  test('respects negated patterns', async () => {
+    await writeFiles(['dist/old.js', 'dist/keep.js'])
+
+    await clean('dist', ['dist', '!dist/keep.js'])
+
+    expect(await fsExists(path.join(cwd, 'dist/old.js'))).toBe(false)
+    expect(await fsExists(path.join(cwd, 'dist/keep.js'))).toBe(true)
+  })
+})
diff --git a/src/features/clean.ts b/src/features/clean.ts
index 5ab936b03..66e285c30 100644
--- a/src/features/clean.ts
+++ b/src/features/clean.ts
@@ -1,6 +1,6 @@
 import path from 'node:path'
 import { createDebug } from 'obug'
-import { glob } from 'tinyglobby'
+import { glob, isDynamicPattern } from 'tinyglobby'
 import { fsRemove } from '../utils/fs.ts'
 import { slash } from '../utils/general.ts'
 import { globalLogger } from '../utils/logger.ts'
@@ -25,16 +25,41 @@ export async function cleanOutDir(configs: ResolvedConfig[]): Promise<void> {
     }
 
     if (!config.clean.length) continue
-    const files = await glob(config.clean, {
-      cwd: config.cwd,
-      absolute: true,
-      onlyFiles: false,
-      dot: true,
-    })
 
-    const normalizedOutDir = config.outDir.replace(RE_LAST_SLASH, '')
+    // Matching a literal `outDir` pattern from `cwd` makes the glob list `cwd`
+    // itself, so list only the contents of `outDir` instead. Negated patterns
+    // can exclude files inside `outDir`, so keep the combined glob for them.
+    const outDir = path.resolve(config.outDir)
+    const scopeToOutDir = config.clean.every(
+      (pattern) => !pattern.startsWith('!'),
+    )
+    let cleansOutDir = false
+    const patterns: string[] = []
+    for (const pattern of config.clean) {
+      if (
+        scopeToOutDir &&
+        !isDynamicPattern(pattern) &&
+        path.resolve(config.cwd, pattern) === outDir
+      ) {
+        cleansOutDir = true
+      } else {
+        patterns.push(pattern)
+      }
+    }
+
+    const globOptions = { absolute: true, onlyFiles: false, dot: true }
+    const files: string[] = []
+    if (cleansOutDir) {
+      files.push(...(await glob('**', { ...globOptions, cwd: outDir })))
+    }
+    if (patterns.length) {
+      files.push(...(await glob(patterns, { ...globOptions, cwd: config.cwd })))
+    }
+
+    // Glob results use forward slashes, so compare them in the same form
+    const normalizedOutDir = slash(config.outDir).replace(RE_LAST_SLASH, '')
     for (const file of files) {
-      const normalizedFile = file.replace(RE_LAST_SLASH, '')
+      const normalizedFile = slash(file).replace(RE_LAST_SLASH, '')
       if (normalizedFile !== normalizedOutDir) {
         removes.add(file)
       }