diff --git a/.gitignore b/.gitignore
index 0dcf79c4604..f72ea1ac514 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,8 +36,8 @@ compile_commands.json
 platform/windows/godot_res.res
 
 # Ninja build files
-build.ninja
-.ninja
+*.ninja
+.ninja/
 run_ninja_env.bat
 
 # Generated by Godot binary
diff --git a/SConstruct b/SConstruct
index 234a6624f1c..7c7d3d25a0d 100644
--- a/SConstruct
+++ b/SConstruct
@@ -1050,7 +1050,7 @@ if env["ninja"]:
     SetOption("experimental", "ninja")
     env["NINJA_FILE_NAME"] = env["ninja_file"]
     env["NINJA_DISABLE_AUTO_RUN"] = not env["ninja_auto_run"]
-    env.Tool("ninja", "build.ninja")
+    env.Tool("ninja", env["ninja_file"])
 
 # Threads
 if env["threads"]:
@@ -1112,7 +1112,7 @@ atexit.register(print_elapsed_time)
 
 
 def purge_flaky_files():
-    paths_to_keep = ["build.ninja"]
+    paths_to_keep = [env["ninja_file"]]
     for build_failure in GetBuildFailures():
         path = build_failure.node.path
         if os.path.isfile(path) and path not in paths_to_keep: