diff --git a/scripts/hooks/config-protection.js b/scripts/hooks/config-protection.js
index 8dce8b2ea..a6aa9180e 100644
--- a/scripts/hooks/config-protection.js
+++ b/scripts/hooks/config-protection.js
@@ -157,9 +157,32 @@ function run(inputOrRaw, options = {}) {
   }
 
   const input = parseInput(inputOrRaw);
-  const filePath = input?.tool_input?.file_path || input?.tool_input?.file || '';
-  if (!filePath) return { exitCode: 0 };
+  for (const filePath of targetPaths(input?.tool_input)) {
+    const blocked = checkTarget(filePath);
+    if (blocked) return blocked;
+  }
+  return { exitCode: 0 };
+}
 
+/**
+ * Every path the tool call would write. A MultiEdit entry may carry its own
+ * `file_path`; one without falls back to the top-level path, the same rule
+ * GateGuard applies (#3761). Checking only the top-level path let a batch
+ * edit an existing config through `edits[].file_path`.
+ */
+function targetPaths(toolInput) {
+  const shared = toolInput?.file_path || toolInput?.file || '';
+  const paths = new Set();
+  if (typeof shared === 'string' && shared) paths.add(shared);
+  const edits = Array.isArray(toolInput?.edits) ? toolInput.edits : [];
+  for (const edit of edits) {
+    const entryPath = edit && typeof edit === 'object' ? edit.file_path : undefined;
+    if (typeof entryPath === 'string' && entryPath) paths.add(entryPath);
+  }
+  return [...paths];
+}
+
+function checkTarget(filePath) {
   const basename = path.basename(filePath);
   // Match case-insensitively. Every PROTECTED_FILES entry is lowercase, and on
   // case-insensitive filesystems (macOS APFS/HFS+, Windows NTFS) a write to
@@ -194,7 +217,7 @@ function run(inputOrRaw, options = {}) {
     }
 
     if (!exists) {
-      return { exitCode: 0 };
+      return null;
     }
 
     return {
@@ -207,7 +230,7 @@ function run(inputOrRaw, options = {}) {
     };
   }
 
-  return { exitCode: 0 };
+  return null;
 }
 
 module.exports = { run };
diff --git a/tests/hooks/config-protection.test.js b/tests/hooks/config-protection.test.js
index 9ab7d844f..8f766ff3c 100644
--- a/tests/hooks/config-protection.test.js
+++ b/tests/hooks/config-protection.test.js
@@ -466,6 +466,57 @@ function runTests() {
     })
   );
 
+  results.push(
+    test('blocks a MultiEdit whose existing config target is only in edits[].file_path (#3761)', () => {
+      return withOwnedDirectory(fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-config-protect-multi-')), tmpDir => {
+        const ruff = path.join(tmpDir, 'ruff.toml');
+        const eslintrc = path.join(tmpDir, '.eslintrc.json');
+        fs.writeFileSync(ruff, '{}');
+        fs.writeFileSync(eslintrc, '{}');
+        const ordinary = path.join(tmpDir, 'app.py');
+
+        const perEntryOnly = runHook({
+          tool_name: 'MultiEdit',
+          tool_input: { edits: [{ file_path: ruff, old_string: '{}', new_string: '{ }' }] }
+        });
+        assert.strictEqual(perEntryOnly.code, 2, 'per-entry-only batch should be blocked: ' + perEntryOnly.stderr);
+        assert.ok(perEntryOnly.stderr.includes('BLOCKED: Modifying ruff.toml is not allowed.'), perEntryOnly.stderr);
+
+        const mixed = runHook({
+          tool_name: 'MultiEdit',
+          tool_input: {
+            file_path: ordinary,
+            edits: [
+              { old_string: 'a', new_string: 'b' },
+              { file_path: eslintrc, old_string: '{}', new_string: '{ }' }
+            ]
+          }
+        });
+        assert.strictEqual(mixed.code, 2, 'mixed ordinary/config batch should be blocked: ' + mixed.stderr);
+        assert.ok(mixed.stderr.includes('BLOCKED: Modifying .eslintrc.json is not allowed.'), mixed.stderr);
+      });
+    })
+  );
+
+  results.push(
+    test('allows a MultiEdit that only creates or touches non-protected files', () => {
+      return withOwnedDirectory(fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-config-protect-multi-ok-')), tmpDir => {
+        const result = runHook({
+          tool_name: 'MultiEdit',
+          tool_input: {
+            file_path: path.join(tmpDir, 'app.py'),
+            edits: [
+              { old_string: 'a', new_string: 'b' },
+              { file_path: path.join(tmpDir, 'lib.py'), old_string: 'a', new_string: 'b' },
+              { file_path: path.join(tmpDir, 'ruff.toml'), old_string: '', new_string: '[lint]' }
+            ]
+          }
+        });
+        assert.strictEqual(result.code, 0, 'batch with no existing protected target should pass: ' + result.stderr);
+      });
+    })
+  );
+
   results.push(
     test('does not block build or test tooling configs', () => {
       // Pins the boundary: this hook guards LINTER configs. A future widening