diff --git a/graphql/codegen/src/__tests__/codegen/expand-targets.test.ts b/graphql/codegen/src/__tests__/codegen/expand-targets.test.ts
index 6d405cf4b..60a552631 100644
--- a/graphql/codegen/src/__tests__/codegen/expand-targets.test.ts
+++ b/graphql/codegen/src/__tests__/codegen/expand-targets.test.ts
@@ -2,7 +2,7 @@ import * as fs from 'node:fs';
 import * as os from 'node:os';
 import * as path from 'node:path';
 
-import { expandApiNamesToMultiTarget, expandSchemaDirToMultiTarget, removeStaleTargetDirs } from '../../core/generate';
+import { expandApiNamesToMultiTarget, expandSchemaDirToMultiTarget, removeStaleTargetDirs, TARGETS_MANIFEST } from '../../core/generate';
 
 describe('expandApiNamesToMultiTarget', () => {
   it('returns null for no apiNames', () => {
@@ -151,7 +151,13 @@ describe('removeStaleTargetDirs', () => {
     fs.rmSync(tempDir, { recursive: true, force: true });
   });
 
-  it('removes directories not in current target list', () => {
+  /** Write a .targets manifest listing the given names. */
+  function writeManifest(names: string[]) {
+    fs.writeFileSync(path.join(tempDir, TARGETS_MANIFEST), JSON.stringify(names));
+  }
+
+  it('removes previous targets that are no longer current', () => {
+    writeManifest(['admin', 'auth', 'public', 'objects']);
     fs.mkdirSync(path.join(tempDir, 'admin'));
     fs.mkdirSync(path.join(tempDir, 'auth'));
     fs.mkdirSync(path.join(tempDir, 'public'));
@@ -166,14 +172,30 @@ describe('removeStaleTargetDirs', () => {
     expect(fs.existsSync(path.join(tempDir, 'objects'))).toBe(false);
   });
 
-  it('preserves files (only removes directories)', () => {
+  it('preserves directories not listed in manifest', () => {
+    writeManifest(['admin', 'auth']);
     fs.mkdirSync(path.join(tempDir, 'admin'));
-    fs.writeFileSync(path.join(tempDir, 'index.ts'), 'export {}');
+    fs.mkdirSync(path.join(tempDir, 'auth'));
+    fs.mkdirSync(path.join(tempDir, 'config'));
+    fs.mkdirSync(path.join(tempDir, 'utils'));
+
+    const removed = removeStaleTargetDirs(tempDir, ['admin']);
+
+    expect(removed).toEqual(['auth']);
+    expect(fs.existsSync(path.join(tempDir, 'admin'))).toBe(true);
+    expect(fs.existsSync(path.join(tempDir, 'auth'))).toBe(false);
+    expect(fs.existsSync(path.join(tempDir, 'config'))).toBe(true);
+    expect(fs.existsSync(path.join(tempDir, 'utils'))).toBe(true);
+  });
+
+  it('returns empty array when no manifest exists', () => {
+    fs.mkdirSync(path.join(tempDir, 'admin'));
+    fs.mkdirSync(path.join(tempDir, 'config'));
 
     const removed = removeStaleTargetDirs(tempDir, ['admin']);
 
     expect(removed).toEqual([]);
-    expect(fs.existsSync(path.join(tempDir, 'index.ts'))).toBe(true);
+    expect(fs.existsSync(path.join(tempDir, 'config'))).toBe(true);
   });
 
   it('returns empty array when output root does not exist', () => {
@@ -181,7 +203,8 @@ describe('removeStaleTargetDirs', () => {
     expect(removed).toEqual([]);
   });
 
-  it('returns empty array when no stale directories exist', () => {
+  it('returns empty array when no stale targets exist', () => {
+    writeManifest(['admin', 'auth']);
     fs.mkdirSync(path.join(tempDir, 'admin'));
     fs.mkdirSync(path.join(tempDir, 'auth'));
 
@@ -189,7 +212,8 @@ describe('removeStaleTargetDirs', () => {
     expect(removed).toEqual([]);
   });
 
-  it('removes all directories when target list is empty', () => {
+  it('removes all previous targets when current list is empty', () => {
+    writeManifest(['old-target']);
     fs.mkdirSync(path.join(tempDir, 'old-target'));
 
     const removed = removeStaleTargetDirs(tempDir, []);
@@ -197,4 +221,12 @@ describe('removeStaleTargetDirs', () => {
     expect(removed).toEqual(['old-target']);
     expect(fs.existsSync(path.join(tempDir, 'old-target'))).toBe(false);
   });
+
+  it('handles corrupt manifest gracefully', () => {
+    fs.writeFileSync(path.join(tempDir, TARGETS_MANIFEST), 'not json');
+    fs.mkdirSync(path.join(tempDir, 'admin'));
+
+    const removed = removeStaleTargetDirs(tempDir, []);
+    expect(removed).toEqual([]);
+  });
 });
diff --git a/graphql/codegen/src/core/generate.ts b/graphql/codegen/src/core/generate.ts
index 026d117f6..7e2ace908 100644
--- a/graphql/codegen/src/core/generate.ts
+++ b/graphql/codegen/src/core/generate.ts
@@ -626,9 +626,14 @@ function applySharedPgpmDb(
   };
 }
 
+/** Manifest file listing generated target names, written to the output root. */
+export const TARGETS_MANIFEST = '.targets';
+
 /**
- * Remove subdirectories in `outputRoot` that are not in `currentTargetNames`.
- * Useful for cleaning up stale target output before a fresh multi-target generate.
+ * Remove stale generated target directories from `outputRoot`.
+ * Reads the `.targets` manifest (written by `generateMulti`) to know which
+ * directories were previously generated. Only those are eligible for removal;
+ * hand-written directories (e.g. `config/`, `utils/`) are never touched.
  * Returns the list of directory names that were removed.
  */
 export function removeStaleTargetDirs(
@@ -639,14 +644,26 @@ export function removeStaleTargetDirs(
   const removed: string[] = [];
   if (!fs.existsSync(outputRoot)) return removed;
 
+  const manifestPath = path.join(outputRoot, TARGETS_MANIFEST);
+  if (!fs.existsSync(manifestPath)) return removed;
+
+  let previousTargets: string[];
+  try {
+    previousTargets = JSON.parse(fs.readFileSync(manifestPath, 'utf-8'));
+  } catch {
+    return removed;
+  }
+
   const currentTargets = new Set(currentTargetNames);
-  const entries = fs.readdirSync(outputRoot, { withFileTypes: true });
-  for (const entry of entries) {
-    if (entry.isDirectory() && !currentTargets.has(entry.name)) {
-      fs.rmSync(path.join(outputRoot, entry.name), { recursive: true, force: true });
-      removed.push(entry.name);
+  const staleTargets = previousTargets.filter((t) => !currentTargets.has(t));
+
+  for (const target of staleTargets) {
+    const dirPath = path.join(outputRoot, target);
+    if (fs.existsSync(dirPath)) {
+      fs.rmSync(dirPath, { recursive: true, force: true });
+      removed.push(target);
       if (verbose) {
-        console.log(`Removed stale target directory: ${entry.name}`);
+        console.log(`Removed stale target directory: ${target}`);
       }
     }
   }
@@ -833,6 +850,12 @@ export async function generateMulti(
         [],
         { pruneStaleFiles: false },
       );
+
+      // Write manifest so removeStaleTargetDirs knows which dirs are generated
+      fs.writeFileSync(
+        path.join(outputRoot, TARGETS_MANIFEST),
+        JSON.stringify(successfulNames.sort()) + '\n',
+      );
     }
   }
 
diff --git a/graphql/codegen/src/index.ts b/graphql/codegen/src/index.ts
index a8a417da4..4d54cb5be 100644
--- a/graphql/codegen/src/index.ts
+++ b/graphql/codegen/src/index.ts
@@ -23,7 +23,7 @@ export { defineConfig } from './types/config';
 
 // Main generate function (orchestrates the entire pipeline)
 export type { GenerateOptions, GenerateResult, GenerateMultiOptions, GenerateMultiResult } from './core/generate';
-export { generate, generateMulti, expandApiNamesToMultiTarget, expandSchemaDirToMultiTarget, removeStaleTargetDirs } from './core/generate';
+export { generate, generateMulti, expandApiNamesToMultiTarget, expandSchemaDirToMultiTarget, removeStaleTargetDirs, TARGETS_MANIFEST } from './core/generate';
 
 // Config utilities
 export { findConfigFile, loadConfigFile } from './core/config';