diff --git a/dev-packages/node-integration-tests/suites/modules/scenario-isolated.js b/dev-packages/node-integration-tests/suites/modules/scenario-isolated.js
new file mode 100644
index 000000000000..ec543d39824e
--- /dev/null
+++ b/dev-packages/node-integration-tests/suites/modules/scenario-isolated.js
@@ -0,0 +1,14 @@
+const { loggingTransport } = require('@sentry-internal/node-integration-tests');
+const Sentry = require('@sentry/node');
+
+Sentry.init({
+  dsn: 'https://public@dsn.ingest.sentry.io/1337',
+  release: '1.0',
+  transport: loggingTransport,
+});
+
+// `test.ts` writes these packages in the folders where the isolated layouts of pnpm and Bun keep them
+require('./node_modules/.pnpm/pnpm-isolated-package@1.2.3/node_modules/pnpm-isolated-package');
+require('./node_modules/.bun/bun-isolated-package@4.5.6/node_modules/bun-isolated-package');
+
+Sentry.captureException(new Error('error_1'));
diff --git a/dev-packages/node-integration-tests/suites/modules/test.ts b/dev-packages/node-integration-tests/suites/modules/test.ts
index f47c4c1f8b09..709bc24ddb1a 100644
--- a/dev-packages/node-integration-tests/suites/modules/test.ts
+++ b/dev-packages/node-integration-tests/suites/modules/test.ts
@@ -1,4 +1,5 @@
 import { SDK_VERSION } from '@sentry/core';
+import { mkdirSync, rmSync, writeFileSync } from 'fs';
 import { join } from 'path';
 import { afterAll, describe, expect, test } from 'vitest';
 import { cleanupChildProcesses, createRunner } from '../../utils/runner';
@@ -27,6 +28,28 @@ describe('modulesIntegration', () => {
     await runner.completed();
   });
 
+  test('CJS with the isolated layouts of pnpm and Bun', async () => {
+    const nodeModulesDir = join(__dirname, 'node_modules');
+    for (const [storeDir, name, version] of [
+      ['.pnpm', 'pnpm-isolated-package', '1.2.3'],
+      ['.bun', 'bun-isolated-package', '4.5.6'],
+    ] as const) {
+      const packageDir = join(nodeModulesDir, storeDir, `${name}@${version}`, 'node_modules', name);
+      mkdirSync(packageDir, { recursive: true });
+      writeFileSync(join(packageDir, 'package.json'), JSON.stringify({ name, version }));
+      writeFileSync(join(packageDir, 'index.js'), 'module.exports = {};');
+    }
+
+    try {
+      await createRunner(__dirname, 'scenario-isolated.js')
+        .expect({ event: { modules: { 'pnpm-isolated-package': '1.2.3', 'bun-isolated-package': '4.5.6' } } })
+        .start()
+        .completed();
+    } finally {
+      rmSync(nodeModulesDir, { recursive: true, force: true });
+    }
+  });
+
   test('ESM', async () => {
     const runner = createRunner(__dirname, 'server.mjs')
       .withInstrument(join(__dirname, 'instrument.mjs'))
diff --git a/packages/node/src/integrations/modules.ts b/packages/node/src/integrations/modules.ts
index 508bae1beace..90921f75388b 100644
--- a/packages/node/src/integrations/modules.ts
+++ b/packages/node/src/integrations/modules.ts
@@ -1,5 +1,5 @@
 import { existsSync, readFileSync } from 'node:fs';
-import { dirname, join } from 'node:path';
+import { basename, dirname, join } from 'node:path';
 import { GLOBAL_OBJ, type IntegrationFn } from '@sentry/core';
 
 type ModuleInfo = Record<string, string>;
@@ -73,6 +73,24 @@ function collectModules(): ModuleInfo {
   };
 }
 
+/**
+ * Whether `dir` is a node_modules folder of the main module, or a folder
+ * `<that node_modules>/<.pnpm or .bun>/<package id>/node_modules`, where the isolated layouts of pnpm and Bun keep
+ * each package.
+ */
+function isMainModulesDir(dir: string, mainPaths: string[]): boolean {
+  if (mainPaths.includes(dir)) {
+    return true;
+  }
+
+  const storeDir = dirname(dirname(dir));
+  return (
+    basename(dir) === 'node_modules' &&
+    ['.pnpm', '.bun'].includes(basename(storeDir)) &&
+    mainPaths.includes(dirname(storeDir))
+  );
+}
+
 /** Extract information about package.json modules from require.cache */
 function collectRequireModules(): ModuleInfo {
   const mainPaths = require.main?.paths || [];
@@ -94,7 +112,7 @@ function collectRequireModules(): ModuleInfo {
       if (!dir || orig === dir || seen.has(orig)) {
         return undefined;
       }
-      if (mainPaths.indexOf(dir) < 0) {
+      if (!isMainModulesDir(dir, mainPaths)) {
         return updir();
       }