diff --git a/test/jslib/test_jslib_custom_settings.out b/test/jslib/test_jslib_custom_settings.out
deleted file mode 100644
index d00491fd7e5bb..0000000000000
--- a/test/jslib/test_jslib_custom_settings.out
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/test/test_jslib.py b/test/test_jslib.py
index 0c46710abc217..e4677f2a4a946 100644
--- a/test/test_jslib.py
+++ b/test/test_jslib.py
@@ -354,7 +354,10 @@ def test_jslib_legacy(self):
   # See https://github.com/emscripten-core/emscripten/issues/10580.
   def test_jslib_custom_settings(self):
     self.cflags += ['--js-library', test_file('jslib/test_jslib_custom_settings.js'), '-jsDCUSTOM_JS_OPTION=1']
-    self.do_run_in_out_file_test('jslib/test_jslib_custom_settings.c')
+    self.do_runf('jslib/test_jslib_custom_settings.c', '1\n')
+
+    # verify that the settings can be specified more than once, and that the last one wins.
+    self.do_runf('jslib/test_jslib_custom_settings.c', '2\n', cflags=['-jsDCUSTOM_JS_OPTION=2'])
 
     self.assert_fail([EMCC, '-jsDWASM=0'], 'cannot change built-in settings values with a -jsD directive')
 
diff --git a/tools/cmdline.py b/tools/cmdline.py
index d708a09f5c5a7..dd025f0d0f9ba 100644
--- a/tools/cmdline.py
+++ b/tools/cmdline.py
@@ -216,6 +216,7 @@ def parse_args(newargs):  # noqa: C901, PLR0912, PLR0915
   """
   should_exit = False
   skip = False
+  user_js_defines = set()
   LEGACY_ARGS = {'--js-opts', '--llvm-opts', '--llvm-lto', '--memory-init-file'}
   LEGACY_FLAGS = {'--separate-asm', '--jcache', '--proxy-to-worker', '--default-obj-ext',
                   '--embind-emit-tsd', '--remove-duplicates', '--no-heap-copy'}
@@ -575,8 +576,9 @@ def consume_arg_file():
         key, value = key.split('=')
       else:
         value = '1'
-      if key in settings.keys():
+      if key in settings.keys() and key not in user_js_defines:
         exit_with_error(f'{arg}: cannot change built-in settings values with a -jsD directive. Pass -s{key}={value} instead!')
+      user_js_defines.add(key)
       # Apply user -jsD settings
       settings[key] = value
       newargs[i] = ''