--- a/testing/marionette/components/marionette.js
+++ b/testing/marionette/components/marionette.js
@@ -150,21 +150,31 @@ MarionetteComponent.prototype = {
 MarionetteComponent.prototype.handle = function(cmdLine) {
   if (cmdLine.handleFlag("marionette", false)) {
     this.enabled = true;
   }
 };
 
 MarionetteComponent.prototype.observe = function(subject, topic, data) {
   switch (topic) {
+    case "command-line-startup":
+      Services.obs.removeObserver(this, topic);
+      this.handle(subject);
+
     case "profile-after-change":
       // Using sessionstore-windows-restored as the xpcom category doesn't
       // seem to work, so we wait for that by adding an observer here.
       Services.obs.addObserver(this, "sessionstore-windows-restored");
 
+      // In safe mode the command line handlers are getting parsed after the
+      // safe mode dialog has been closed. To allow Marionette to start
+      // earlier, register the CLI startup observer notification for
+      // special-cased handlers, which gets fired before the dialog appears.
+      Services.obs.addObserver(this, "command-line-startup");
+
       prefs.readFromEnvironment(ENV_PRESERVE_PREFS);
 
       if (this.enabled) {
         // We want to suppress the modal dialog that's shown
         // when starting up in safe-mode to enable testing.
         if (Services.appinfo.inSafeMode) {
           Services.obs.addObserver(this, "domwindowopened");
         }
@@ -224,16 +234,17 @@ MarionetteComponent.prototype.setupLogge
   logger.addAppender(new Log.DumpAppender());
   return logger;
 };
 
 MarionetteComponent.prototype.suppressSafeModeDialog = function(win) {
   win.addEventListener("load", () => {
     if (win.document.getElementById("safeModeDialog")) {
       // accept the dialog to start in safe-mode
+      this.logger.debug("Safe Mode detected. Going to suspress the dialog now.");
       win.setTimeout(() => {
         win.document.documentElement.getButton("accept").click();
       });
     }
   }, {once: true});
 };
 
 MarionetteComponent.prototype.init = function() {

new file mode 100644
--- /dev/null
+++ b/testing/marionette/harness/marionette_harness/tests/unit/test_cli_arguments.py
@@ -0,0 +1,36 @@
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+import copy
+
+from marionette_harness import MarionetteTestCase
+
+
+class TestCommandLineArguments(MarionetteTestCase):
+
+    def setUp(self):
+        super(TestCommandLineArguments, self).setUp()
+
+        self.orig_arguments = copy.copy(self.marionette.instance.app_args)
+
+    def tearDown(self):
+        self.marionette.instance.app_args = self.orig_arguments
+        self.marionette.quit(clean=True)
+
+        super(TestCommandLineArguments, self).tearDown()
+
+    def test_start_in_safe_mode(self):
+        self.marionette.instance.app_args.append("-safe-mode")
+
+        self.marionette.quit()
+        self.marionette.start_session()
+
+        with self.marionette.using_context("chrome"):
+            safe_mode = self.marionette.execute_script("""
+              Cu.import("resource://gre/modules/Services.jsm");
+
+              return Services.appinfo.inSafeMode;
+            """)
+
+            self.assertTrue(safe_mode, "Safe Mode has not been enabled")

--- a/testing/marionette/harness/marionette_harness/tests/unit/unit-tests.ini
+++ b/testing/marionette/harness/marionette_harness/tests/unit/unit-tests.ini
@@ -1,9 +1,11 @@
 [test_marionette.py]
+[test_cli_arguments.py]
+skip-if = manage_instance == false || appname == 'fennec' # Bug 1298921 and bug 1322993
 [test_geckoinstance.py]
 [test_data_driven.py]
 [test_session.py]
 [test_capabilities.py]
 [test_accessibility.py]
 [test_expectedfail.py]
 expected = fail
 [test_click.py]