diff --git a/packages/analytics/modules/analytics/index.ts b/packages/analytics/modules/analytics/index.ts
index 07af9a307..c0eddc258 100644
--- a/packages/analytics/modules/analytics/index.ts
+++ b/packages/analytics/modules/analytics/index.ts
@@ -73,9 +73,8 @@ export const analytics = createAnalytics(useAppConfig().analytics);
       }
     });
 
-    // Ensure analytics is initialized in every context, mainly the background.
-    // TODO: Once there's a way to filter which entrypoints a plugin is applied to, only apply this to the background
-    addWxtPlugin(wxt, pluginModuleId);
+    // Ensure analytics is initialized in the background only.
+    addWxtPlugin(wxt, pluginModuleId, (entry) => entry.type === 'background');
 
     // Fix issues with dependencies
     addViteConfig(wxt, () => ({
diff --git a/packages/wxt/e2e/tests/modules.test.ts b/packages/wxt/e2e/tests/modules.test.ts
index 56ef03849..4bc710f24 100644
--- a/packages/wxt/e2e/tests/modules.test.ts
+++ b/packages/wxt/e2e/tests/modules.test.ts
@@ -243,6 +243,77 @@ describe('Module Helpers', () => {
 
       await expect(project.serializeOutput()).resolves.toContain(expectedText);
     });
+
+    it('should apply plugins only to entrypoints matching their filter', async () => {
+      const project = new TestProject();
+      project.addFile(
+        'entrypoints/background.ts',
+        'export default defineBackground(() => {})',
+      );
+      project.addFile(
+        'entrypoints/content.ts',
+        `
+          export default defineContentScript({
+            matches: ["*://*/*"],
+            main: () => {},
+          })
+        `,
+      );
+      project.addFile('entrypoints/popup/index.html', '<html></html>');
+      project.addFile('entrypoints/options/index.html', '<html></html>');
+
+      const backgroundPluginPath = project.addFile(
+        'modules/test/background-plugin.ts',
+        `export default defineWxtPlugin(() => console.log("BACKGROUND_PLUGIN"))`,
+      );
+      const popupPluginPath = project.addFile(
+        'modules/test/popup-plugin.ts',
+        `export default defineWxtPlugin(() => console.log("POPUP_PLUGIN"))`,
+      );
+      project.addFile(
+        'modules/test.ts',
+        `
+          import { defineWxtModule, addWxtPlugin } from 'wxt/modules';
+
+          export default defineWxtModule((wxt) => {
+            addWxtPlugin(wxt, "${normalizePath(backgroundPluginPath)}", (entrypoint) => entrypoint.type === 'background');
+            addWxtPlugin(wxt, "${normalizePath(popupPluginPath)}", (entrypoint) => entrypoint.name === 'popup');
+          });
+        `,
+      );
+
+      await project.build();
+
+      await expect(
+        project.serializeFile('.output/chrome-mv3/background.js'),
+      ).resolves.toContain('BACKGROUND_PLUGIN');
+      await expect(
+        project.serializeFile('.output/chrome-mv3/content-scripts/content.js'),
+      ).resolves.not.toContain('BACKGROUND_PLUGIN');
+
+      const getInjectedScript = async (htmlFile: string) => {
+        const html = await readFile(
+          project.resolvePath('.output/chrome-mv3', htmlFile),
+          'utf-8',
+        );
+        const match = html.match(/<script[^>]*\ssrc="([^"]+)"/);
+        if (!match) throw Error(`No script tag in ${htmlFile}`);
+        return readFile(
+          project.resolvePath(
+            '.output/chrome-mv3',
+            match[1].replace(/^\//, ''),
+          ),
+          'utf-8',
+        );
+      };
+
+      await expect(getInjectedScript('popup.html')).resolves.toContain(
+        'POPUP_PLUGIN',
+      );
+      await expect(getInjectedScript('options.html')).resolves.not.toContain(
+        'POPUP_PLUGIN',
+      );
+    });
   });
 
   describe('imports', () => {
diff --git a/packages/wxt/e2e/tests/output-structure.test.ts b/packages/wxt/e2e/tests/output-structure.test.ts
index 8dd06e61d..7d9b3a34b 100644
--- a/packages/wxt/e2e/tests/output-structure.test.ts
+++ b/packages/wxt/e2e/tests/output-structure.test.ts
@@ -381,7 +381,7 @@ describe('Output Directory Structure', () => {
       .toMatchInlineSnapshot(`
         ".output/chrome-mv3/background.js
         ----------------------------------------
-        import { n as logHello } from "./chunks/_virtual_wxt-plugins-BdnAIYoG.js";
+        import { t as logHello } from "./chunks/log-DNePel8J.js";
         function defineBackground(arg) {
         	if (arg == null || typeof arg === "function") return { main: arg };
         	return arg;
diff --git a/packages/wxt/src/internal/builders/vite/index.ts b/packages/wxt/src/internal/builders/vite/index.ts
index 2ad47772a..149884a20 100644
--- a/packages/wxt/src/internal/builders/vite/index.ts
+++ b/packages/wxt/src/internal/builders/vite/index.ts
@@ -198,13 +198,11 @@ export class ViteBuilder implements WxtBuilder {
     config.plugins ??= [];
     config.plugins.push(
       wxtPlugins.devHtmlPrerender(this.config, server),
-      wxtPlugins.resolveVirtualModules(this.config),
       wxtPlugins.devServerGlobals(this.config, server),
       wxtPlugins.tsconfigPaths(this.config),
       wxtPlugins.noopBackground(),
       wxtPlugins.addRuntimeEnvEntries(this.config),
       wxtPlugins.defineImportMeta(),
-      wxtPlugins.wxtPluginLoader(this.config),
       wxtPlugins.resolveAppConfig(this.config),
     );
     if (
diff --git a/packages/wxt/src/internal/builders/vite/plugins/__tests__/wxt-plugin-loader.test.ts b/packages/wxt/src/internal/builders/vite/plugins/__tests__/wxt-plugin-loader.test.ts
new file mode 100644
index 000000000..7ae99088b
--- /dev/null
+++ b/packages/wxt/src/internal/builders/vite/plugins/__tests__/wxt-plugin-loader.test.ts
@@ -0,0 +1,36 @@
+import { describe, expect, it } from 'vitest';
+import { getPluginModules } from '../wxt-plugin-loader';
+import {
+  fakeBackgroundEntrypoint,
+  fakeContentScriptEntrypoint,
+} from '../../../../../internal-utils/testing/fake-objects';
+import type { WxtPluginEntry } from '../../../../../types';
+
+describe('Plugin Loader', () => {
+  describe('getPluginModules', () => {
+    const background = fakeBackgroundEntrypoint();
+    const contentScript = fakeContentScriptEntrypoint();
+
+    it('includes plugins without an apply function', () => {
+      const plugins: WxtPluginEntry[] = [{ module: 'a' }];
+      expect(getPluginModules(plugins, background)).toEqual(['a']);
+    });
+
+    it('includes only plugins whose apply function returns true', () => {
+      const plugins: WxtPluginEntry[] = [
+        { module: 'a', apply: (entry) => entry.type === 'background' },
+        { module: 'b', apply: (entry) => entry.type === 'content-script' },
+      ];
+      expect(getPluginModules(plugins, background)).toEqual(['a']);
+      expect(getPluginModules(plugins, contentScript)).toEqual(['b']);
+    });
+
+    it('includes every plugin when the entrypoint is unresolved', () => {
+      const plugins: WxtPluginEntry[] = [
+        { module: 'a', apply: () => false },
+        { module: 'b' },
+      ];
+      expect(getPluginModules(plugins, undefined)).toEqual(['a', 'b']);
+    });
+  });
+});
diff --git a/packages/wxt/src/internal/builders/vite/plugins/resolve-virtual-modules.ts b/packages/wxt/src/internal/builders/vite/plugins/resolve-virtual-modules.ts
index ae041257f..1c006f383 100644
--- a/packages/wxt/src/internal/builders/vite/plugins/resolve-virtual-modules.ts
+++ b/packages/wxt/src/internal/builders/vite/plugins/resolve-virtual-modules.ts
@@ -3,6 +3,7 @@ import { resolve } from 'path';
 import type { Plugin } from 'vite';
 import { ResolvedConfig } from '../../../../types';
 import { normalizePath } from '../../../../internal-utils/path-utils';
+import { getEntrypointName } from '../../../../internal-utils/entrypoint-utils';
 import { VirtualModuleId, virtualModuleNames } from '../../../virtual-modules';
 
 /**
@@ -37,7 +38,16 @@ export function resolveVirtualModules(config: ResolvedConfig): Plugin[] {
             resolve(config.wxtModuleDir, `dist/virtual/${name}.mjs`),
             'utf-8',
           );
-          return template.replace(`virtual:user-${name}`, inputPath);
+          const entrypointName = getEntrypointName(
+            config.entrypointsDir,
+            inputPath,
+          );
+          return template
+            .replace(`virtual:user-${name}`, inputPath)
+            .replace(
+              'virtual:wxt-plugins',
+              `virtual:wxt-plugins?entrypoint=${encodeURIComponent(entrypointName)}`,
+            );
         },
       },
     };
diff --git a/packages/wxt/src/internal/builders/vite/plugins/wxt-plugin-loader.ts b/packages/wxt/src/internal/builders/vite/plugins/wxt-plugin-loader.ts
index 3943458a1..a6a01bd44 100644
--- a/packages/wxt/src/internal/builders/vite/plugins/wxt-plugin-loader.ts
+++ b/packages/wxt/src/internal/builders/vite/plugins/wxt-plugin-loader.ts
@@ -1,58 +1,101 @@
 import { parseHTML } from 'linkedom';
 import type * as vite from 'vite';
 import { normalizePath } from '../../../../internal-utils/path-utils';
-import { ResolvedConfig } from '../../../../types';
+import { getEntrypointName } from '../../../../internal-utils/entrypoint-utils';
+import { Entrypoint, ResolvedConfig, WxtPluginEntry } from '../../../../types';
+
+export function getPluginModules(
+  plugins: Array<string | WxtPluginEntry>,
+  entrypoint: Entrypoint | undefined,
+): string[] {
+  return plugins
+    .map(
+      (plugin): WxtPluginEntry =>
+        typeof plugin === 'string' ? { module: plugin } : plugin,
+    )
+    .filter(
+      (plugin) => entrypoint == null || (plugin.apply?.(entrypoint) ?? true),
+    )
+    .map((plugin) => plugin.module);
+}
 
 /**
  * Resolve and load plugins for each entrypoint. This handles both JS
  * entrypoints via the `virtual:wxt-plugins` import, and HTML files by adding
- * `virtual:wxt-html-plugins` to the document's `<head>`
+ * `virtual:wxt-html-plugins` to the document's `<head>`. Accepts an optional
+ * `?entrypoint=<name>` query to evaluate plugin `apply` hooks per request.
+ *
+ * @param getEntrypoints Returns the most recently resolved entrypoints.
+ *   Injected by the caller instead of read from a global, so this plugin
+ *   doesn't depend on global `wxt` state.
  */
-export function wxtPluginLoader(config: ResolvedConfig): vite.Plugin {
+export function wxtPluginLoader(
+  config: ResolvedConfig,
+  getEntrypoints: () => Entrypoint[],
+): vite.Plugin {
   const virtualModuleId = 'virtual:wxt-plugins';
   const resolvedVirtualModuleId = '\0' + virtualModuleId;
   const virtualHtmlModuleId = 'virtual:wxt-html-plugins';
   const resolvedVirtualHtmlModuleId = '\0' + virtualHtmlModuleId;
 
+  function getEntrypointFromId(id: string): Entrypoint | undefined {
+    const queryIndex = id.indexOf('?');
+    if (queryIndex === -1) return undefined;
+    const entrypointNameFromQueryParam = new URLSearchParams(
+      id.slice(queryIndex),
+    ).get('entrypoint');
+    if (!entrypointNameFromQueryParam) return undefined;
+    return getEntrypoints().find(
+      (entry) => entry.name === entrypointNameFromQueryParam,
+    );
+  }
+
   return {
     name: 'wxt:plugin-loader',
     resolveId: {
       filter: {
         id: [
-          new RegExp(`^${virtualModuleId}$`),
-          new RegExp(`^${virtualHtmlModuleId}$`),
+          new RegExp(`^${virtualModuleId}`),
+          new RegExp(`^${virtualHtmlModuleId}`),
         ],
       },
       handler(id) {
-        if (id === virtualModuleId) {
-          return resolvedVirtualModuleId;
-        }
-
-        return resolvedVirtualHtmlModuleId;
+        return '\0' + id;
       },
     },
     load: {
       filter: {
         id: [
-          new RegExp(`^${resolvedVirtualModuleId}$`),
-          new RegExp(`^${resolvedVirtualHtmlModuleId}$`),
+          new RegExp(`^${resolvedVirtualModuleId}`),
+          new RegExp(`^${resolvedVirtualHtmlModuleId}`),
         ],
       },
       handler(id) {
-        if (id === resolvedVirtualModuleId) {
-          // Import and init all plugins
-          const imports = config.plugins
+        const bareId = id.slice(1);
+        const entrypoint = getEntrypointFromId(bareId);
+
+        if (
+          bareId === virtualModuleId ||
+          bareId.startsWith(`${virtualModuleId}?`)
+        ) {
+          // Import and init only the plugins that apply to this entrypoint
+          const modules = getPluginModules(config.plugins, entrypoint);
+          const imports = modules
             .map(
-              (plugin, i) =>
-                `import initPlugin${i} from '${normalizePath(plugin)}';`,
+              (module, i) =>
+                `import initPlugin${i} from '${normalizePath(module)}';`,
             )
             .join('\n');
-          const initCalls = config.plugins
+          const initCalls = modules
             .map((_, i) => `  initPlugin${i}();`)
             .join('\n');
           return `${imports}\n\nexport function initPlugins() {\n${initCalls}\n}`;
         } else {
-          return `import { initPlugins } from '${virtualModuleId}';
+          // Forward resolved entrypoint to match the JS module.
+          const jsModuleId = entrypoint
+            ? `${virtualModuleId}?entrypoint=${encodeURIComponent(entrypoint.name)}`
+            : virtualModuleId;
+          return `import { initPlugins } from '${jsModuleId}';
             try {
               initPlugins();
             } catch (err) {
@@ -64,11 +107,23 @@ export function wxtPluginLoader(config: ResolvedConfig): vite.Plugin {
     transformIndexHtml: {
       // Use "pre" so the new script is added before vite bundles all the scripts
       order: 'pre',
-      handler(html, _ctx) {
+      handler(html, ctx) {
+        const entrypointName = getEntrypointName(
+          config.entrypointsDir,
+          ctx.filename,
+        );
+        const entrypoint = getEntrypoints().find(
+          (entry) => entry.name === entrypointName,
+        );
+        const query = entrypoint
+          ? `?entrypoint=${encodeURIComponent(entrypoint.name)}`
+          : '';
+        const htmlModuleId = `${virtualHtmlModuleId}${query}`;
+
         const src =
           config.command === 'serve'
-            ? `${config.dev.server?.origin}/@id/${virtualHtmlModuleId}`
-            : virtualHtmlModuleId;
+            ? `${config.dev.server?.origin}/@id/${htmlModuleId}`
+            : htmlModuleId;
 
         const { document } = parseHTML(html);
         const existing = document.querySelector(`script[src='${src}']`);
diff --git a/packages/wxt/src/internal/builtin-modules/index.ts b/packages/wxt/src/internal/builtin-modules/index.ts
index 4617e8925..3d5a02bb4 100644
--- a/packages/wxt/src/internal/builtin-modules/index.ts
+++ b/packages/wxt/src/internal/builtin-modules/index.ts
@@ -2,9 +2,11 @@ import { WxtModule } from '../../types';
 import faviconPermission from './favicon-permission';
 import unimport from './unimport';
 import escapeUnicode from './escape-unicode';
+import plugins from './plugins';
 
 export const builtinModules: WxtModule<any>[] = [
   unimport,
   faviconPermission,
   escapeUnicode,
+  plugins,
 ];
diff --git a/packages/wxt/src/internal/builtin-modules/plugins.ts b/packages/wxt/src/internal/builtin-modules/plugins.ts
new file mode 100644
index 000000000..15a552463
--- /dev/null
+++ b/packages/wxt/src/internal/builtin-modules/plugins.ts
@@ -0,0 +1,26 @@
+import { addViteConfig, defineWxtModule } from '../../modules';
+import type { Entrypoint } from '../../types';
+import { resolveVirtualModules } from '../builders/vite/plugins/resolve-virtual-modules';
+import { wxtPluginLoader } from '../builders/vite/plugins/wxt-plugin-loader';
+
+/**
+ * Owns the virtual `wxt-plugins`/`wxt-html-plugins` modules used by
+ * `addWxtPlugin`. Keeps the latest resolved entrypoints in module-local state
+ * instead of on the global `wxt` object.
+ */
+export default defineWxtModule({
+  name: 'wxt:built-in:plugins',
+  setup(wxt) {
+    let entrypoints: Entrypoint[] = [];
+    wxt.hooks.hook('entrypoints:resolved', (_, resolved) => {
+      entrypoints = resolved;
+    });
+
+    addViteConfig(wxt, () => ({
+      plugins: [
+        resolveVirtualModules(wxt.config),
+        wxtPluginLoader(wxt.config, () => entrypoints),
+      ],
+    }));
+  },
+});
diff --git a/packages/wxt/src/modules/index.ts b/packages/wxt/src/modules/index.ts
index 14b4e7116..6a739a121 100644
--- a/packages/wxt/src/modules/index.ts
+++ b/packages/wxt/src/modules/index.ts
@@ -129,16 +129,26 @@ export function addViteConfig(
  *
  * @example
  *   export default defineWxtModule((wxt) => {
- *     addWxtPlugin(wxt, 'wxt-module-analytics/client-plugin');
+ *     addWxtPlugin(
+ *       wxt,
+ *       'wxt-module-analytics/background-plugin',
+ *       (entrypoint) => entrypoint.type === 'background',
+ *     );
  *   });
  *
  * @param wxt The wxt instance provided by the module's setup function.
  * @param plugin An import from an NPM module, or an absolute file path to the
  *   file to load at runtime.
+ * @param apply Optional. Return `true` to load the plugin in the given
+ *   entrypoint. Defaults to loading the plugin in every entrypoint.
  */
-export function addWxtPlugin(wxt: Wxt, plugin: string): void {
+export function addWxtPlugin(
+  wxt: Wxt,
+  plugin: string,
+  apply?: (entrypoint: Entrypoint) => boolean,
+): void {
   wxt.hooks.hook('config:resolved', (wxt) => {
-    wxt.config.plugins.push(plugin);
+    wxt.config.plugins.push({ module: plugin, apply });
   });
 }
 
diff --git a/packages/wxt/src/types.ts b/packages/wxt/src/types.ts
index 1e2b9b477..b4e389f87 100644
--- a/packages/wxt/src/types.ts
+++ b/packages/wxt/src/types.ts
@@ -1681,13 +1681,28 @@ export interface ResolvedConfig {
   builtinModules: WxtModule<any>[];
   userModules: WxtModuleWithMetadata<any>[];
   /**
-   * An array of string to import plugins from. These paths should be resolvable
-   * by vite, and they should `export default defineWxtPlugin(...)`.
+   * Plugins registered via `addWxtPlugin`. Each entry's `module` should be
+   * resolvable by vite, and should `export default defineWxtPlugin(...)`. An
+   * optional `apply` function restricts which entrypoints the plugin loads in.
    *
    * @example
-   *   ['@wxt-dev/module-vue/plugin', 'wxt-module-google-analytics/plugin'];
+   *   [{ module: '@wxt-dev/module-vue/plugin' }];
    */
-  plugins: string[];
+  plugins: Array<string | WxtPluginEntry>;
+}
+
+/**
+ * A plugin registered via `addWxtPlugin`, along with an optional `apply`
+ * function controlling which entrypoints it's loaded in.
+ */
+export interface WxtPluginEntry {
+  /** Import path or absolute file path to the plugin module. */
+  module: string;
+  /**
+   * Return `true` to include the plugin in this entrypoint. When omitted, the
+   * plugin is included in every entrypoint.
+   */
+  apply?: (entrypoint: Entrypoint) => boolean;
 }
 
 export interface FsCache {