diff --git a/docs/guide/essentials/config/typescript.md b/docs/guide/essentials/config/typescript.md
index 8d939e2e..2bfa8b1d 100644
--- a/docs/guide/essentials/config/typescript.md
+++ b/docs/guide/essentials/config/typescript.md
@@ -17,28 +17,14 @@ Or if you're in a monorepo, you may not want to extend the config. If you don't
 /// <reference path="./.wxt/wxt.d.ts" />
 ```
 
-## Compiler Options
-
-To specify custom compiler options, add them in `<rootDir>/tsconfig.json`:
-
-```jsonc
-// <rootDir>/tsconfig.json
-{
-  "extends": ".wxt/tsconfig.json",
-  "compilerOptions": {
-    "jsx": "preserve",
-  },
-}
-```
-
 ## TSConfig Paths
 
 WXT provides a default set of path aliases.
 
 | Alias | To            | Example                                         |
 | ----- | ------------- | ----------------------------------------------- |
-| `~~`  | `<rootDir>/*` | `import "~~/scripts"`                           |
-| `@@`  | `<rootDir>/*` | `import "@@/scripts"`                           |
+| `~~`  | `<rootDir>/*` | `import "~~/package.json"`                      |
+| `@@`  | `<rootDir>/*` | `import "@@/package.json"`                      |
 | `~`   | `<srcDir>/*`  | `import { toLowerCase } from "~/utils/strings"` |
 | `@`   | `<srcDir>/*`  | `import { toLowerCase } from "@/utils/strings"` |
 
@@ -63,3 +49,34 @@ export default defineConfig({
 import { fakeTab } from 'testing/fake-objects';
 import { toLowerCase } from 'strings';
 ```
+
+## Custom Options
+
+To specify custom compiler or top-level options, you have two options:
+
+1. Override WXT's value completely by setting it in your root `tsconfig.json`:
+
+   ```jsonc
+   // <rootDir>/tsconfig.json
+   {
+     "extends": ".wxt/tsconfig.json",
+     "compilerOptions": {
+       "jsx": "preserve",
+     },
+   }
+   ```
+
+2. Merge custom values into values generated by WXT via the `prepare:tsconfig` hook:
+
+   ```ts
+   // wxt.config.ts
+   export default defineConfig({
+     hooks: {
+       'prepare:tsconfig': (wxt, { tsconfig }) => {
+         tsconfig.compilerOptions.lib.push('WebWorker');
+       },
+     },
+   });
+   ```
+
+Overriding is great for simple boolean values, but not for complex options like `paths` or `libs`, where you can't just "add" a value to the object from your `tsconfig.json` file. So WXT provides the hook that let's you add or merge or delete or do whatever you want to the config file before it's written to the `.wxt/` directory.
diff --git a/packages/wxt/e2e/tests/hooks.test.ts b/packages/wxt/e2e/tests/hooks.test.ts
index 47ecb109..613a0b6f 100644
--- a/packages/wxt/e2e/tests/hooks.test.ts
+++ b/packages/wxt/e2e/tests/hooks.test.ts
@@ -6,6 +6,7 @@ const hooks: WxtHooks = {
   ready: vi.fn(),
   'config:resolved': vi.fn(),
   'prepare:types': vi.fn(),
+  'prepare:tsconfig': vi.fn(),
   'prepare:publicPaths': vi.fn(),
   'build:before': vi.fn(),
   'build:done': vi.fn(),
@@ -56,6 +57,7 @@ describe('Hooks', () => {
       ready: true,
       'config:resolved': true,
       'prepare:types': true,
+      'prepare:tsconfig': true,
       'prepare:publicPaths': true,
       'build:before': false,
       'build:done': false,
@@ -88,6 +90,7 @@ describe('Hooks', () => {
       ready: true,
       'config:resolved': true,
       'prepare:types': true,
+      'prepare:tsconfig': true,
       'prepare:publicPaths': true,
       'build:before': true,
       'build:done': true,
@@ -120,6 +123,7 @@ describe('Hooks', () => {
       ready: true,
       'config:resolved': true,
       'prepare:types': true,
+      'prepare:tsconfig': true,
       'prepare:publicPaths': true,
       'build:before': true,
       'build:done': true,
@@ -152,6 +156,7 @@ describe('Hooks', () => {
       ready: true,
       'config:resolved': true,
       'prepare:types': true,
+      'prepare:tsconfig': true,
       'prepare:publicPaths': true,
       'build:before': true,
       'build:done': true,
@@ -191,6 +196,7 @@ describe('Hooks', () => {
       ready: true,
       'config:resolved': true,
       'prepare:types': true,
+      'prepare:tsconfig': true,
       'prepare:publicPaths': true,
       'build:before': true,
       'build:done': true,
diff --git a/packages/wxt/e2e/tests/typescript-project.test.ts b/packages/wxt/e2e/tests/typescript-project.test.ts
index 9710484a..673783ca 100644
--- a/packages/wxt/e2e/tests/typescript-project.test.ts
+++ b/packages/wxt/e2e/tests/typescript-project.test.ts
@@ -1,5 +1,6 @@
 import { describe, it, expect } from 'vitest';
 import { TestProject } from '../utils';
+import { readFile } from 'node:fs/promises';
 
 describe('TypeScript Project', () => {
   it('should generate defined constants correctly', async () => {
@@ -333,25 +334,63 @@ describe('TypeScript Project', () => {
           "strict": true,
           "skipLibCheck": true,
           "paths": {
-            "@": [".."],
-            "@/*": ["../*"],
-            "~": [".."],
-            "~/*": ["../*"],
-            "@@": [".."],
-            "@@/*": ["../*"],
-            "~~": [".."],
-            "~~/*": ["../*"]
+            "@": [
+              ".."
+            ],
+            "@/*": [
+              "../*"
+            ],
+            "~": [
+              ".."
+            ],
+            "~/*": [
+              "../*"
+            ],
+            "@@": [
+              ".."
+            ],
+            "@@/*": [
+              "../*"
+            ],
+            "~~": [
+              ".."
+            ],
+            "~~/*": [
+              "../*"
+            ]
           }
         },
         "include": [
           "../**/*",
           "./wxt.d.ts"
         ],
-        "exclude": ["../.output"]
+        "exclude": [
+          "../**/node_modules",
+          "../.output"
+        ]
       }"
     `);
   });
 
+  it("should allow updating the project's tsconfig via hooks", async () => {
+    const project = new TestProject();
+    project.setConfigFileConfig({});
+    project.addFile('entrypoints/unlisted.html', '<html></html>');
+
+    await project.prepare({
+      hooks: {
+        'prepare:tsconfig': (_, { tsconfig }) => {
+          tsconfig.test = 'test';
+        },
+      },
+    });
+
+    const actual = JSON.parse(
+      await readFile(project.resolvePath('.wxt/tsconfig.json'), 'utf-8'),
+    );
+    expect(actual).toMatchObject({ test: 'test' });
+  });
+
   it('should generate correct path aliases for a custom srcDir', async () => {
     const project = new TestProject();
     project.addFile('src/entrypoints/unlisted.html', '<html></html>');
@@ -377,21 +416,40 @@ describe('TypeScript Project', () => {
           "strict": true,
           "skipLibCheck": true,
           "paths": {
-            "@": ["../src"],
-            "@/*": ["../src/*"],
-            "~": ["../src"],
-            "~/*": ["../src/*"],
-            "@@": [".."],
-            "@@/*": ["../*"],
-            "~~": [".."],
-            "~~/*": ["../*"]
+            "@": [
+              "../src"
+            ],
+            "@/*": [
+              "../src/*"
+            ],
+            "~": [
+              "../src"
+            ],
+            "~/*": [
+              "../src/*"
+            ],
+            "@@": [
+              ".."
+            ],
+            "@@/*": [
+              "../*"
+            ],
+            "~~": [
+              ".."
+            ],
+            "~~/*": [
+              "../*"
+            ]
           }
         },
         "include": [
           "../**/*",
           "./wxt.d.ts"
         ],
-        "exclude": ["../.output"]
+        "exclude": [
+          "../**/node_modules",
+          "../.output"
+        ]
       }"
     `);
   });
@@ -425,23 +483,46 @@ describe('TypeScript Project', () => {
           "strict": true,
           "skipLibCheck": true,
           "paths": {
-            "example": ["../example"],
-            "example/*": ["../example/*"],
-            "@": ["../src"],
-            "@/*": ["../src/*"],
-            "~": ["../src"],
-            "~/*": ["../src/*"],
-            "@@": [".."],
-            "@@/*": ["../*"],
-            "~~": [".."],
-            "~~/*": ["../*"]
+            "example": [
+              "../example"
+            ],
+            "example/*": [
+              "../example/*"
+            ],
+            "@": [
+              "../src"
+            ],
+            "@/*": [
+              "../src/*"
+            ],
+            "~": [
+              "../src"
+            ],
+            "~/*": [
+              "../src/*"
+            ],
+            "@@": [
+              ".."
+            ],
+            "@@/*": [
+              "../*"
+            ],
+            "~~": [
+              ".."
+            ],
+            "~~/*": [
+              "../*"
+            ]
           }
         },
         "include": [
           "../**/*",
           "./wxt.d.ts"
         ],
-        "exclude": ["../.output"]
+        "exclude": [
+          "../**/node_modules",
+          "../.output"
+        ]
       }"
     `);
   });
diff --git a/packages/wxt/src/core/generate-wxt-dir.ts b/packages/wxt/src/core/generate-wxt-dir.ts
index 5ee5e043..05083b98 100644
--- a/packages/wxt/src/core/generate-wxt-dir.ts
+++ b/packages/wxt/src/core/generate-wxt-dir.ts
@@ -283,41 +283,42 @@ async function getTsConfigEntry(): Promise<WxtDirFileEntry> {
     if (res.startsWith('.') || res.startsWith('/')) return res;
     return './' + res;
   };
-  const paths = Object.entries(wxt.config.alias)
-    .flatMap(([alias, absolutePath]) => {
-      const aliasPath = getTsconfigPath(absolutePath);
-      return [
-        `"${alias}": ["${aliasPath}"]`,
-        `"${alias}/*": ["${aliasPath}/*"]`,
-      ];
-    })
-    .map((line) => `      ${line}`)
-    .join(',\n');
 
-  const text = `{
-  "compilerOptions": {
-    "target": "ESNext",
-    "module": "ESNext",
-    "moduleResolution": "Bundler",
-    "noEmit": true,
-    "esModuleInterop": true,
-    "forceConsistentCasingInFileNames": true,
-    "resolveJsonModule": true,
-    "strict": true,
-    "skipLibCheck": true,
-    "paths": {
-${paths}
-    }
-  },
-  "include": [
-    "${getTsconfigPath(wxt.config.root)}/**/*",
-    "./wxt.d.ts"
-  ],
-  "exclude": ["${getTsconfigPath(wxt.config.outBaseDir)}"]
-}`;
+  const paths = Object.fromEntries(
+    Object.entries(wxt.config.alias)
+      .map(([alias, absolutePath]) => [alias, getTsconfigPath(absolutePath)])
+      .flatMap(([alias, path]) => [
+        // Add alias for files
+        [alias, [path]],
+        // Add alias for all files in a directory
+        [alias + '/*', [path + '/*']],
+      ]),
+  );
+
+  const tsconfig = {
+    compilerOptions: {
+      target: 'ESNext',
+      module: 'ESNext',
+      moduleResolution: 'Bundler',
+      noEmit: true,
+      esModuleInterop: true,
+      forceConsistentCasingInFileNames: true,
+      resolveJsonModule: true,
+      strict: true,
+      skipLibCheck: true,
+      paths,
+    },
+    include: [`${getTsconfigPath(wxt.config.root)}/**/*`, './wxt.d.ts'],
+    exclude: [
+      getTsconfigPath(wxt.config.root) + '/**/node_modules',
+      getTsconfigPath(wxt.config.outBaseDir),
+    ],
+  };
+
+  await wxt.hooks.callHook('prepare:tsconfig', wxt, { tsconfig });
 
   return {
     path: 'tsconfig.json',
-    text,
+    text: JSON.stringify(tsconfig, null, 2),
   };
 }
diff --git a/packages/wxt/src/types.ts b/packages/wxt/src/types.ts
index 1cb2aadf..5ebee7c7 100644
--- a/packages/wxt/src/types.ts
+++ b/packages/wxt/src/types.ts
@@ -1259,6 +1259,11 @@ export interface ServerInfo {
   origin: string;
 }
 
+export type PrepareTsconfigs = {
+  /** The JSON contents of the `.wxt/tsconfig.json` file. */
+  tsconfig: any;
+};
+
 export type HookResult = Promise<void> | void;
 
 export interface WxtHooks {
@@ -1298,6 +1303,17 @@ export interface WxtHooks {
    *   });
    */
   'prepare:types': (wxt: Wxt, entries: WxtDirEntry[]) => HookResult;
+  /**
+   * Called before WXT writes your tsconfig to the disk, allowing full
+   * customization by modifying the object by reference.
+   *
+   * @since 0.20.28
+   * @example
+   *   wxt.hooks.hook('prepare:tsconfig', (wxt, { tsconfig }) => {
+   *     tsconfig.compilerOptions.lib.push('WebWorker');
+   *   });
+   */
+  'prepare:tsconfig': (wxt: Wxt, configs: PrepareTsconfigs) => HookResult;
   /**
    * Called before generating the list of public paths inside
    * `.wxt/types/paths.d.ts`. Use this hook to add additional paths (relative to