diff --git a/eos-migrate-chrome-profile b/eos-migrate-chrome-profile
index 5886bcd..6d97298 100755
--- a/eos-migrate-chrome-profile
+++ b/eos-migrate-chrome-profile
@@ -29,6 +29,7 @@ from gi.repository import GLib
 
 
 USER_HOME_DIR = os.path.expanduser("~/")
+DESKTOP_SHORTCUTS_DIR = os.path.join(USER_HOME_DIR, ".local", "share", "applications")
 OLD_CHROME_CONFIG_DIR = os.path.join(USER_HOME_DIR, ".config", "google-chrome")
 NEW_CHROME_DATA_DIR = os.path.join(USER_HOME_DIR, ".var", "app", "com.google.Chrome")
 NEW_CHROME_CONFIG_DIR = os.path.join(NEW_CHROME_DATA_DIR, "config", "google-chrome")
@@ -89,6 +90,43 @@ def update_mimeapps_list(path):
         keyfile.save_to_file(path)
 
 
+def update_desktop_shortcut(path):
+    keyfile = GLib.KeyFile()
+    keyfile.load_from_file(path,
+                           GLib.KeyFileFlags.KEEP_COMMENTS |
+                           GLib.KeyFileFlags.KEEP_TRANSLATIONS)
+
+    groups, _ = keyfile.get_groups()
+    for group in groups:
+        try:
+            exec_cmd = keyfile.get_string(group, "Exec")
+        except GLib.GError as error:
+            if not error.matches(GLib.key_file_error_quark(),
+                                 GLib.KeyFileError.KEY_NOT_FOUND):
+                raise error
+            continue
+
+        if not exec_cmd.startswith("/usr/bin/eos-google-chrome"):
+            continue
+
+        keyfile.set_string(group, "Exec",
+                           "/usr/bin/flatpak run com.google.Chrome" +
+                           exec_cmd[len("/usr/bin/eos-google-chrome"):])
+
+    keyfile.save_to_file(path)
+
+
+def update_desktop_shortcuts(path=DESKTOP_SHORTCUTS_DIR):
+    try:
+        shortcuts = os.listdir(path)
+    except FileNotFoundError:
+        return
+
+    for filename in shortcuts:
+        if filename.endswith(".desktop"):
+            update_desktop_shortcut(os.path.join(path, filename))
+
+
 def update_old_config_references(path):
     if not os.path.isfile(path):
         return
@@ -107,6 +145,7 @@ def main():
         sys.exit(1)
 
     update_mimeapps_list(MIMEAPPS_LIST)
+    update_desktop_shortcuts()
 
     if (
         os.path.isdir(OLD_CHROME_CONFIG_DIR) and
diff --git a/tests/test_migrate_chrome_profile.py b/tests/test_migrate_chrome_profile.py
index 1a977e3..ee6b447 100644
--- a/tests/test_migrate_chrome_profile.py
+++ b/tests/test_migrate_chrome_profile.py
@@ -91,6 +91,126 @@ def _test(self, orig_data, expected_data):
         self.assertEqual(expected_data, new_data)
 
 
+class TestUpdateDesktopShortcuts(BaseTestCase):
+    def setUp(self):
+        super().setUp()
+
+        self.tmp = tempfile.TemporaryDirectory()
+
+    def tearDown(self):
+        self.tmp.cleanup()
+
+    def test_no_shortcuts_dir(self):
+        emfp.update_desktop_shortcuts(os.path.join(self.tmp.name, "no-such-directory"))
+
+    def test_empty_shortcuts_dir(self):
+        emfp.update_desktop_shortcuts(self.tmp.name)
+
+    def test_not_there(self):
+        orig_data = textwrap.dedent(
+            """
+            [Desktop Entry]
+            Exec=/usr/bin/chromium-browser --profile-directory=Default
+            """
+        ).lstrip()
+        expected_data = orig_data
+
+        self._test(orig_data, expected_data)
+
+    def test_there(self):
+        orig_data = textwrap.dedent(
+            """
+            #!/usr/bin/env xdg-open
+            [Desktop Entry]
+            Version=1.0
+            Terminal=false
+            Type=Application
+            Name=YouTube
+            Exec=/usr/bin/eos-google-chrome "--profile-directory=Profile 1"
+            Icon=chrome-agimnkijcaahngcdmfeangaknmldooml-Profile_1
+            StartupWMClass=crx_agimnkijcaahngcdmfeangaknmldooml
+            Actions=Explore;Subscriptions
+
+            [Desktop Action Explore]
+            Name=Explore
+            Exec=/usr/bin/eos-google-chrome "--profile-directory=Profile 1"
+
+            [Desktop Action Subscriptions]
+            Name=Subscriptions
+            Exec=/usr/bin/eos-google-chrome "--profile-directory=Profile 1"
+            """
+        ).lstrip()
+        expected_data = textwrap.dedent(
+            """
+            #!/usr/bin/env xdg-open
+            [Desktop Entry]
+            Version=1.0
+            Terminal=false
+            Type=Application
+            Name=YouTube
+            Exec=/usr/bin/flatpak run com.google.Chrome "--profile-directory=Profile 1"
+            Icon=chrome-agimnkijcaahngcdmfeangaknmldooml-Profile_1
+            StartupWMClass=crx_agimnkijcaahngcdmfeangaknmldooml
+            Actions=Explore;Subscriptions
+
+            [Desktop Action Explore]
+            Name=Explore
+            Exec=/usr/bin/flatpak run com.google.Chrome "--profile-directory=Profile 1"
+
+            [Desktop Action Subscriptions]
+            Name=Subscriptions
+            Exec=/usr/bin/flatpak run com.google.Chrome "--profile-directory=Profile 1"
+            """
+        ).lstrip()
+
+        self._test(orig_data, expected_data)
+
+    def test_multi_languages(self):
+        orig_data = textwrap.dedent(
+            """
+            # Comment
+            [Desktop Entry]
+            Name=Chrome
+            Name[en_GB]=Chrome, milord
+            Exec=/usr/bin/eos-google-chrome --profile-directory=Default
+            """
+        ).lstrip()
+        expected_data = textwrap.dedent(
+            """
+            # Comment
+            [Desktop Entry]
+            Name=Chrome
+            Name[en_GB]=Chrome, milord
+            Exec=/usr/bin/flatpak run com.google.Chrome --profile-directory=Default
+            """
+        ).lstrip()
+
+        self._test(orig_data, expected_data)
+
+    def test_no_exec_in_group(self):
+        orig_data = textwrap.dedent(
+            """
+            [Dummy Group]
+            foo=bar
+            """
+        ).lstrip()
+        expected_data = orig_data
+
+        self._test(orig_data, expected_data)
+
+    def _test(self, orig_data, expected_data):
+        test_desktop = os.path.join(self.tmp.name,
+                                    "test.desktop")
+        with open(test_desktop, "w") as f:
+            f.write(orig_data)
+
+        emfp.update_desktop_shortcuts(self.tmp.name)
+        with open(test_desktop, "r") as f:
+            new_data = f.read()
+
+        self.assertEqual(expected_data, new_data)
+
+
 class TestUpdateOldConfigReferences(BaseTestCase):
     def setUp(self):
         super().setUp()