diff --git a/packages/wxt/e2e/tests/zip.test.ts b/packages/wxt/e2e/tests/zip.test.ts
index 3ff265aad..c370097bc 100644
--- a/packages/wxt/e2e/tests/zip.test.ts
+++ b/packages/wxt/e2e/tests/zip.test.ts
@@ -285,4 +285,26 @@ describe('Zipping', () => {
       expect(await project.fileExists(sourcesZip)).toBe(false);
     },
   );
+
+  it('should include files in the zip when negated in zip.exclude', async () => {
+    const project = new TestProject({
+      name: 'test',
+      version: '1.0.0',
+    });
+    project.addFile(
+      'entrypoints/background.ts',
+      'export default defineBackground(() => {});',
+    );
+    const unzipDir = project.resolvePath('.output/test-1.0.0-chrome');
+    const sourcesZip = project.resolvePath('.output/test-1.0.0-chrome.zip');
+
+    await project.zip({
+      zip: {
+        exclude: ['**/*.json', '!manifest.json'],
+      },
+    });
+
+    await extract(sourcesZip, { dir: unzipDir });
+    expect(await project.fileExists(unzipDir, 'manifest.json')).toBe(true);
+  });
 });
diff --git a/packages/wxt/src/core/utils/__tests__/minimatch-multiple.test.ts b/packages/wxt/src/core/utils/__tests__/minimatch-multiple.test.ts
new file mode 100644
index 000000000..34c078e13
--- /dev/null
+++ b/packages/wxt/src/core/utils/__tests__/minimatch-multiple.test.ts
@@ -0,0 +1,46 @@
+import { describe, it, expect } from 'vitest';
+import { minimatchMultiple } from '../minimatch-multiple';
+
+describe('minimatchMultiple', () => {
+  it('should return false if the pattern array is undefined', () => {
+    const patterns = undefined;
+    const search = 'test.json';
+
+    expect(minimatchMultiple(search, patterns)).toBe(false);
+  });
+
+  it('should return false if the pattern array is empty', () => {
+    const patterns: string[] = [];
+    const search = 'test.json';
+
+    expect(minimatchMultiple(search, patterns)).toBe(false);
+  });
+
+  it('should return true if the pattern array contains a match', () => {
+    const patterns = ['test.yml', 'test.json'];
+    const search = 'test.json';
+
+    expect(minimatchMultiple(search, patterns)).toBe(true);
+  });
+
+  it('should return false if the pattern array does not contain a match', () => {
+    const patterns = ['test.yml', 'test.json'];
+    const search = 'test.txt';
+
+    expect(minimatchMultiple(search, patterns)).toBe(false);
+  });
+
+  it('should return false if the pattern matches a negative pattern', () => {
+    const patterns = ['test.*', '!test.json'];
+    const search = 'test.json';
+
+    expect(minimatchMultiple(search, patterns)).toBe(false);
+  });
+
+  it('should return false if the pattern matches a negative pattern, regardless of order', () => {
+    const patterns = ['!test.json', 'test.*'];
+    const search = 'test.json';
+
+    expect(minimatchMultiple(search, patterns)).toBe(false);
+  });
+});
diff --git a/packages/wxt/src/core/utils/minimatch-multiple.ts b/packages/wxt/src/core/utils/minimatch-multiple.ts
new file mode 100644
index 000000000..be1bbf0e8
--- /dev/null
+++ b/packages/wxt/src/core/utils/minimatch-multiple.ts
@@ -0,0 +1,40 @@
+import { minimatch, MinimatchOptions } from 'minimatch';
+
+/**
+ * Run [`minimatch`](https://npmjs.com/package/minimatch) against multiple
+ * patterns.
+ *
+ * Supports negated patterns, the order does not matter. If your `search` string
+ * matches any of the negative patterns, it will return `false`.
+ *
+ * @example
+ * ```ts
+ * minimatchMultiple('a.json', ['*.json', '!b.json']); // => true
+ * minimatchMultiple('b.json', ['*.json', '!b.json']); // => false
+ * ```
+ */
+export function minimatchMultiple(
+  search: string,
+  patterns: string[] | undefined,
+  options?: MinimatchOptions,
+): boolean {
+  if (patterns == null) return false;
+
+  const negatePatterns: string[] = [];
+  const positivePatterns: string[] = [];
+  for (const pattern of patterns) {
+    if (pattern[0] === '!') negatePatterns.push(pattern.slice(1));
+    else positivePatterns.push(pattern);
+  }
+
+  if (
+    negatePatterns.some((negatePattern) =>
+      minimatch(search, negatePattern, options),
+    )
+  )
+    return false;
+
+  return positivePatterns.some((positivePattern) =>
+    minimatch(search, positivePattern, options),
+  );
+}
diff --git a/packages/wxt/src/core/zip.ts b/packages/wxt/src/core/zip.ts
index ceda07efd..70626d6ae 100644
--- a/packages/wxt/src/core/zip.ts
+++ b/packages/wxt/src/core/zip.ts
@@ -3,7 +3,6 @@ import path from 'node:path';
 import fs from 'fs-extra';
 import { safeFilename } from './utils/strings';
 import { getPackageJson } from './utils/package';
-import { minimatch } from 'minimatch';
 import { formatDuration } from './utils/time';
 import { printFileList } from './utils/log/printFileList';
 import { findEntrypoints, internalBuild } from './utils/building';
@@ -11,6 +10,7 @@ import { registerWxt, wxt } from './wxt';
 import JSZip from 'jszip';
 import glob from 'fast-glob';
 import { normalizePath } from './utils/paths';
+import { minimatchMultiple } from './utils/minimatch-multiple';
 
 /**
  * Build and zip the extension for distribution.
@@ -122,8 +122,8 @@ async function zipDir(
     })
   ).filter((relativePath) => {
     return (
-      options?.include?.some((pattern) => minimatch(relativePath, pattern)) ||
-      !options?.exclude?.some((pattern) => minimatch(relativePath, pattern))
+      minimatchMultiple(relativePath, options?.include) ||
+      !minimatchMultiple(relativePath, options?.exclude)
     );
   });
   const filesToZip = [