diff --git a/data/com.github.devalien.workspaces.appdata.xml.in b/data/com.github.devalien.workspaces.appdata.xml.in
index a040316..9f0c16c 100644
--- a/data/com.github.devalien.workspaces.appdata.xml.in
+++ b/data/com.github.devalien.workspaces.appdata.xml.in
@@ -67,6 +67,16 @@
   </content_rating>
 
   <releases>
+  <release version="1.2.1" date="2020-08-21">
+      <description>
+        <p>Bug Fixes</p>
+        <ul>
+          <li>Fixed shortcut for flatpak</li>
+          <li>Fixed load apps for flatpak</li>
+        </ul>
+      </description>
+    </release>
+
     <release version="1.2.0" date="2020-08-21">
       <description>
         <p>Features</p>
diff --git a/debian/changelog b/debian/changelog
index 9d6ae83..f54f3b9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+com.github.devalien.workspaces (1.2.1) RELEASED; urgency=low
+
+  * Fixed shortcut for flatpak. *
+  * Fixed load apps for flatpak. *
+
+ -- Goncalo Margalho <g@margalho.info>  Mon, 21 Aug 2020 12:20:20 +0200
+
 com.github.devalien.workspaces (1.2.0) RELEASED; urgency=low
 
   * Added default shortcut to launch the app and a way to modify it. *
diff --git a/src/Application.vala b/src/Application.vala
index 3eeaf49..e79c549 100644
--- a/src/Application.vala
+++ b/src/Application.vala
@@ -30,6 +30,7 @@ public class Workspaces.Application : Gtk.Application {
     public const string APP_VERSION = "1.2.0";
     public const string APP_ID = "com.github.devalien.workspaces";
     public const string SHOW_WORKSPACES_CMD = APP_ID;
+    public const string FLATPAK_SHOW_WORKSPACES_CMD = "flatpak run " + APP_ID;
     private const string SHOW_WORKSPACES_SHORTCUT = "<Control><Alt>w";
 
     private bool show_quick_launch = false;
@@ -195,15 +196,26 @@ public class Workspaces.Application : Gtk.Application {
     private void set_default_shortcut () {
         CustomShortcutSettings.init ();
         foreach (var shortcut in CustomShortcutSettings.list_custom_shortcuts ()) {
-            if (shortcut.command == SHOW_WORKSPACES_CMD) {
-                CustomShortcutSettings.edit_shortcut (shortcut.relocatable_schema, SHOW_WORKSPACES_SHORTCUT);
-                return;
+            if (is_flatpak ()) {
+                if (shortcut.command == FLATPAK_SHOW_WORKSPACES_CMD) {
+                    CustomShortcutSettings.edit_shortcut (shortcut.relocatable_schema, SHOW_WORKSPACES_SHORTCUT);
+                    return;
+                }
+            } else {
+                if (shortcut.command == SHOW_WORKSPACES_CMD) {
+                    CustomShortcutSettings.edit_shortcut (shortcut.relocatable_schema, SHOW_WORKSPACES_SHORTCUT);
+                    return;
+                }
             }
         }
         var shortcut = CustomShortcutSettings.create_shortcut ();
         if (shortcut != null) {
             CustomShortcutSettings.edit_shortcut (shortcut, SHOW_WORKSPACES_SHORTCUT);
-            CustomShortcutSettings.edit_command (shortcut, SHOW_WORKSPACES_CMD);
+            if (is_flatpak ()) {
+                CustomShortcutSettings.edit_command (shortcut, FLATPAK_SHOW_WORKSPACES_CMD);
+            } else {
+                CustomShortcutSettings.edit_command (shortcut, SHOW_WORKSPACES_CMD);
+            }
         }
     }
 
diff --git a/src/Dialogs/Preferences.vala b/src/Dialogs/Preferences.vala
index af3053c..1ce7520 100644
--- a/src/Dialogs/Preferences.vala
+++ b/src/Dialogs/Preferences.vala
@@ -78,17 +78,34 @@ public class Workspaces.Dialogs.Preferences : Gtk.Dialog {
 
         CustomShortcutSettings.init ();
         foreach (var shortcut in CustomShortcutSettings.list_custom_shortcuts ()) {
-            if (shortcut.command == Workspaces.Application.SHOW_WORKSPACES_CMD) {
-                accel = shortcut.shortcut;
-                accel_path = shortcut.relocatable_schema;
+            if (is_flatpak ()) {
+                if (shortcut.command == Workspaces.Application.FLATPAK_SHOW_WORKSPACES_CMD) {
+                    accel = shortcut.shortcut;
+                    accel_path = shortcut.relocatable_schema;
+                }
+            } else {
+                if (shortcut.command == Workspaces.Application.SHOW_WORKSPACES_CMD) {
+                    accel = shortcut.shortcut;
+                    accel_path = shortcut.relocatable_schema;
+                }
             }
         }
 
         var paste_shortcut_label = create_label (_ ("Open Workspaces Shortcut:"));
         var paste_shortcut_entry = new Workspaces.Widgets.ShortcutEntry (accel);
         paste_shortcut_entry.shortcut_changed.connect ((new_shortcut) => {
-            if (accel_path != null) {
+            if (accel_path != null && accel_path != "") {
                 CustomShortcutSettings.edit_shortcut (accel_path, new_shortcut);
+            } else {
+                var shortcut = CustomShortcutSettings.create_shortcut ();
+                if (shortcut != null) {
+                    CustomShortcutSettings.edit_shortcut (shortcut, new_shortcut);
+                    if (is_flatpak ()) {
+                        CustomShortcutSettings.edit_command (shortcut, Workspaces.Application.FLATPAK_SHOW_WORKSPACES_CMD);
+                    } else {
+                        CustomShortcutSettings.edit_command (shortcut, Workspaces.Application.SHOW_WORKSPACES_CMD);
+                    }
+                }
             }
         });
         if (first_run) {
diff --git a/src/PreferencesWindow.vala b/src/PreferencesWindow.vala
index 6f7dbbc..5b18c93 100644
--- a/src/PreferencesWindow.vala
+++ b/src/PreferencesWindow.vala
@@ -201,9 +201,16 @@ public class Workspaces.PreferencesWindow : Gtk.ApplicationWindow {
 
         CustomShortcutSettings.init ();
         foreach (var shortcut in CustomShortcutSettings.list_custom_shortcuts ()) {
-            if (shortcut.command == Workspaces.Application.SHOW_WORKSPACES_CMD) {
-                accel = shortcut.shortcut;
-                accel_path = shortcut.relocatable_schema;
+            if (is_flatpak ()) {
+                if (shortcut.command == Workspaces.Application.FLATPAK_SHOW_WORKSPACES_CMD) {
+                    accel = shortcut.shortcut;
+                    accel_path = shortcut.relocatable_schema;
+                }
+            } else {
+                if (shortcut.command == Workspaces.Application.SHOW_WORKSPACES_CMD) {
+                    accel = shortcut.shortcut;
+                    accel_path = shortcut.relocatable_schema;
+                }
             }
         }