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..29f9e62decca
--- /dev/null
+++ b/dev-packages/node-integration-tests/suites/modules/scenario-isolated.js
@@ -0,0 +1,18 @@
+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('pnpm-isolated-package');
+require('@pnpm-isolated/scoped-package');
+require('bun-isolated-package');
+require('@bun-isolated/scoped-package');
+// Another version of `pnpm-isolated-package`, loaded last as a dependency of the app would load it
+require('./node_modules/.pnpm/pnpm-isolated-package@1.0.0/node_modules/pnpm-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..57c221f9f7f0 100644
--- a/dev-packages/node-integration-tests/suites/modules/test.ts
+++ b/dev-packages/node-integration-tests/suites/modules/test.ts
@@ -1,5 +1,6 @@
 import { SDK_VERSION } from '@sentry/core';
-import { join } from 'path';
+import { mkdirSync, rmSync, symlinkSync, writeFileSync } from 'fs';
+import { dirname, join } from 'path';
 import { afterAll, describe, expect, test } from 'vitest';
 import { cleanupChildProcesses, createRunner } from '../../utils/runner';
 
@@ -27,6 +28,46 @@ 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, linked] of [
+      ['.pnpm', 'pnpm-isolated-package', '1.2.3', true],
+      // Only a dependency of the app uses this version, so it is not linked into `node_modules`
+      ['.pnpm', 'pnpm-isolated-package', '1.0.0', false],
+      ['.pnpm', '@pnpm-isolated/scoped-package', '2.3.4', true],
+      ['.bun', 'bun-isolated-package', '4.5.6', true],
+      ['.bun', '@bun-isolated/scoped-package', '5.6.7', true],
+    ] as const) {
+      const packageDir = join(nodeModulesDir, storeDir, `${name.replace('/', '+')}@${version}`, 'node_modules', name);
+      mkdirSync(packageDir, { recursive: true });
+      writeFileSync(join(packageDir, 'package.json'), JSON.stringify({ name, version }));
+      writeFileSync(join(packageDir, 'index.js'), 'module.exports = {};');
+
+      if (linked) {
+        mkdirSync(dirname(join(nodeModulesDir, name)), { recursive: true });
+        symlinkSync(packageDir, join(nodeModulesDir, name), 'junction');
+      }
+    }
+
+    try {
+      await createRunner(__dirname, 'scenario-isolated.js')
+        .expect({
+          event: {
+            modules: {
+              'pnpm-isolated-package': '1.2.3',
+              '@pnpm-isolated/scoped-package': '2.3.4',
+              'bun-isolated-package': '4.5.6',
+              '@bun-isolated/scoped-package': '5.6.7',
+            },
+          },
+        })
+        .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..54842d0cd5a3 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 { existsSync, readFileSync, realpathSync } from 'node:fs';
+import { basename, dirname, join } from 'node:path';
 import { GLOBAL_OBJ, type IntegrationFn } from '@sentry/core';
 
 type ModuleInfo = Record<string, string>;
@@ -73,6 +73,34 @@ function collectModules(): ModuleInfo {
   };
 }
 
+/**
+ * Whether `dir` is a node_modules folder of the main module, a folder
+ * `<that node_modules>/<.pnpm or .bun>/<package id>/node_modules`, where the isolated layouts of pnpm and Bun keep
+ * each package, or a scope folder (`@scope`) in one of these folders.
+ */
+function isMainModulesDir(dir: string, mainPaths: string[]): boolean {
+  if (basename(dir).startsWith('@')) {
+    return isMainModulesDir(dirname(dir), mainPaths);
+  }
+
+  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))
+  );
+}
+
+/** Whether `require(name)` in the main module loads the package in `packageDir`. */
+function isResolvedFromMain(name: string, packageDir: string, mainPaths: string[]): boolean {
+  const resolvedDir = mainPaths.map(dir => join(dir, name)).find(dir => existsSync(dir));
+  return !!resolvedDir && realpathSync(resolvedDir) === realpathSync(packageDir);
+}
+
 /** Extract information about package.json modules from require.cache */
 function collectRequireModules(): ModuleInfo {
   const mainPaths = require.main?.paths || [];
@@ -81,6 +109,7 @@ function collectRequireModules(): ModuleInfo {
   // We start with the modules from package.json (if possible)
   // These may be overwritten by more specific versions from the require.cache
   const infos: ModuleInfo = {};
+  const packageDirs: Record<string, string> = {};
   const seen = new Set<string>();
 
   paths.forEach(path => {
@@ -94,7 +123,7 @@ function collectRequireModules(): ModuleInfo {
       if (!dir || orig === dir || seen.has(orig)) {
         return undefined;
       }
-      if (mainPaths.indexOf(dir) < 0) {
+      if (!isMainModulesDir(dir, mainPaths)) {
         return updir();
       }
 
@@ -110,7 +139,12 @@ function collectRequireModules(): ModuleInfo {
           name: string;
           version: string;
         };
-        infos[info.name] = info.version;
+        // The isolated layouts of pnpm and Bun keep every version of a package. Keep the one that the main module loads.
+        const previousDir = packageDirs[info.name];
+        if (!previousDir || !isResolvedFromMain(info.name, previousDir, mainPaths)) {
+          infos[info.name] = info.version;
+          packageDirs[info.name] = orig;
+        }
       } catch {
         // no-empty
       }