diff --git a/marimo/_server/files/directory_scanner.py b/marimo/_server/files/directory_scanner.py
index 447cc05d6d1..d8c60d45c13 100644
--- a/marimo/_server/files/directory_scanner.py
+++ b/marimo/_server/files/directory_scanner.py
@@ -188,6 +188,11 @@ def recurse(directory: str, depth: int = 0) -> list[FileInfo] | None:
             folders: list[FileInfo] = []
 
             for entry in entries:
+                # Check the limit here, not just after adding a file: a
+                # sibling directory's recursion may have reached it.
+                if file_count[0] >= self.max_files:
+                    break
+
                 # Skip hidden files and directories
                 if entry.name.startswith("."):
                     continue
@@ -238,9 +243,6 @@ def recurse(directory: str, depth: int = 0) -> list[FileInfo] | None:
                             files.append(file_info)
                             # Also add to partial results for timeout recovery
                             self.partial_results.append(file_info)
-                            # Check if we've reached the limit
-                            if file_count[0] >= self.max_files:
-                                break
                 except OSError as e:
                     LOGGER.debug(
                         "Error processing entry %s: %s", entry.path, e
diff --git a/tests/_server/test_directory_scanner.py b/tests/_server/test_directory_scanner.py
index c761d3f47cf..c0a9d4b28cb 100644
--- a/tests/_server/test_directory_scanner.py
+++ b/tests/_server/test_directory_scanner.py
@@ -118,6 +118,31 @@ def test_max_files_limit(self, test_dir: Path):
         files = DirectoryScanner(str(test_dir), max_files=5).scan()
         assert _count_files(files) == 5
 
+    def test_max_files_limit_recursion_at_boundary(
+        self, test_dir: Path, monkeypatch: pytest.MonkeyPatch
+    ):
+        """A subdir recursion that reaches max_files must not let another
+        top-level file slip in. Forces the ordering that only flaked in CI."""
+        import marimo._server.files.directory_scanner as scanner_mod
+
+        for i in range(10):
+            _write(test_dir / f"app{i + 3}.py", MARIMO_APP)
+
+        real_scandir = os.scandir
+
+        def ordered_scandir(path: str):  # type: ignore[no-untyped-def]
+            entries = list(real_scandir(path))
+            dirs = [e for e in entries if e.is_dir()]
+            files = sorted(
+                (e for e in entries if not e.is_dir()), key=lambda e: e.name
+            )
+            # 4 files, then the nested dir (reaches the limit), then the rest.
+            return files[:4] + dirs + files[4:]
+
+        monkeypatch.setattr(scanner_mod.os, "scandir", ordered_scandir)
+        files = DirectoryScanner(str(test_dir), max_files=5).scan()
+        assert _count_files(files) == 5
+
     def test_skip_common_directories(self, test_dir: Path):
         skip_names = (
             "venv",