diff --git a/tools/system_libs.py b/tools/system_libs.py
index 3b01a85fbf651..ef896f6ec96ac 100644
--- a/tools/system_libs.py
+++ b/tools/system_libs.py
@@ -471,14 +471,9 @@ def get_files(self):
   def generate_ninja(self, build_dir, libname):
     ensure_sysroot()
     utils.safe_ensure_dirs(build_dir)
+    self.build_dir = build_dir
 
     cflags = self.get_cflags()
-    if self.deterministic_paths:
-      source_dir = utils.path_from_root()
-      relative_source_dir = os.path.relpath(source_dir, build_dir)
-      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
-                 f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}',
-                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     asflags = get_base_cflags(preprocess=False)
     input_files = self.get_files()
     ninja_file = os.path.join(build_dir, 'build.ninja')
@@ -492,17 +487,11 @@ def build_objects(self, build_dir):
     with the `cflags` returned by `self.get_cflags()`.
     """
     batch_inputs = int(os.environ.get('EMCC_BATCH_BUILD', '1'))
+    self.build_dir = build_dir
     batches = {}
     commands = []
     objects = set()
     cflags = self.get_cflags()
-    if self.deterministic_paths:
-      source_dir = utils.path_from_root()
-      if batch_inputs:
-        relative_source_dir = os.path.relpath(source_dir, build_dir)
-        cflags += [f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}']
-      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
-                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     case_insensitive = is_case_insensitive(build_dir)
     for src in self.get_files():
       ext = shared.suffix(src)
@@ -611,6 +600,12 @@ def get_cflags(self):
     if self.includes:
       cflags += ['-I' + utils.path_from_root(i) for i in self._inherit_list('includes')]
 
+    if self.deterministic_paths:
+      source_dir = utils.path_from_root()
+      relative_source_dir = os.path.relpath(source_dir, self.build_dir)
+      cflags += [f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}']
+      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
+                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     return cflags
 
   def get_base_name_prefix(self):