diff --git a/embuilder.py b/embuilder.py
index 4b706c1d6df76..b7752f936a36b 100755
--- a/embuilder.py
+++ b/embuilder.py
@@ -291,7 +291,7 @@ def main():
         library.erase()
       if do_build:
         if USE_NINJA:
-          library.generate()
+          library.generate(deterministic_paths=True)
         else:
           library.build(deterministic_paths=True)
     elif what == 'sysroot':
diff --git a/test/other/codesize/test_codesize_cxx_except.size b/test/other/codesize/test_codesize_cxx_except.size
index c2c735ee85f4b..f802ede453a94 100644
--- a/test/other/codesize/test_codesize_cxx_except.size
+++ b/test/other/codesize/test_codesize_cxx_except.size
@@ -1 +1 @@
-170928
+170950
diff --git a/test/other/codesize/test_codesize_cxx_except_wasm.size b/test/other/codesize/test_codesize_cxx_except_wasm.size
index e5a548bdc8852..dcc00991302e1 100644
--- a/test/other/codesize/test_codesize_cxx_except_wasm.size
+++ b/test/other/codesize/test_codesize_cxx_except_wasm.size
@@ -1 +1 @@
-142143
+142154
diff --git a/test/other/codesize/test_codesize_cxx_except_wasm_exnref.size b/test/other/codesize/test_codesize_cxx_except_wasm_exnref.size
index b3e5808388b4f..61de9cf43ee1e 100644
--- a/test/other/codesize/test_codesize_cxx_except_wasm_exnref.size
+++ b/test/other/codesize/test_codesize_cxx_except_wasm_exnref.size
@@ -1 +1 @@
-144730
+144741
diff --git a/test/other/codesize/test_codesize_cxx_mangle.size b/test/other/codesize/test_codesize_cxx_mangle.size
index d7b5814d237cc..6c8a3c4a397f0 100644
--- a/test/other/codesize/test_codesize_cxx_mangle.size
+++ b/test/other/codesize/test_codesize_cxx_mangle.size
@@ -1 +1 @@
-232437
+232468
diff --git a/tools/system_libs.py b/tools/system_libs.py
index ef896f6ec96ac..73818d8a5b61d 100644
--- a/tools/system_libs.py
+++ b/tools/system_libs.py
@@ -431,8 +431,8 @@ def build(self, deterministic_paths=False):
     self.deterministic_paths = deterministic_paths
     return cache.get(self.get_path(), self.do_build, force=USE_NINJA == 2, quiet=USE_NINJA)
 
-  def generate(self):
-    self.deterministic_paths = False
+  def generate(self, deterministic_paths=False):
+    self.deterministic_paths = deterministic_paths
     return cache.get(self.get_path(), self.do_generate, force=USE_NINJA == 2, quiet=USE_NINJA,
                      deferred=True)
 
@@ -600,12 +600,15 @@ def get_cflags(self):
     if self.includes:
       cflags += ['-I' + utils.path_from_root(i) for i in self._inherit_list('includes')]
 
+    source_dir = utils.path_from_root()
+    relative_source_dir = os.path.relpath(source_dir, self.build_dir)
     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'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}',
                  f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
+    else:
+      cflags += [f'-fmacro-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
+                 f'-fmacro-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}']
     return cflags
 
   def get_base_name_prefix(self):