diff --git a/nixos/modules/installer/cd-dvd/installation-cd-graphical-gnome.nix b/nixos/modules/installer/cd-dvd/installation-cd-graphical-gnome.nix
index 8c98691116dc..803bae4212ef 100644
--- a/nixos/modules/installer/cd-dvd/installation-cd-graphical-gnome.nix
+++ b/nixos/modules/installer/cd-dvd/installation-cd-graphical-gnome.nix
@@ -9,7 +9,14 @@ with lib;
 
   isoImage.edition = "gnome";
 
-  services.xserver.desktopManager.gnome3.enable = true;
+  services.xserver.desktopManager.gnome3 = {
+    # Add firefox to favorite-apps
+    favoriteAppsOverride = ''
+      [org.gnome.shell]
+      favorite-apps=[ 'firefox.desktop', 'org.gnome.Geary.desktop', 'org.gnome.Calendar.desktop', 'org.gnome.Music.desktop', 'org.gnome.Photos.desktop', 'org.gnome.Nautilus.desktop' ]
+    '';
+    enable = true;
+  };
 
   services.xserver.displayManager = {
     gdm = {
diff --git a/nixos/modules/services/desktops/flatpak.nix b/nixos/modules/services/desktops/flatpak.nix
index 7da92cc9f264..d0f6b66328a4 100644
--- a/nixos/modules/services/desktops/flatpak.nix
+++ b/nixos/modules/services/desktops/flatpak.nix
@@ -15,6 +15,18 @@ in {
   options = {
     services.flatpak = {
       enable = mkEnableOption "flatpak";
+
+      guiPackages = mkOption {
+        internal = true;
+        type = types.listOf types.package;
+        default = [];
+        example = literalExample "[ pkgs.gnome3.gnome-software ]";
+        description = ''
+          Packages that provide an interface for flatpak
+          (like gnome-software) that will be automatically available
+          to all users when flatpak is enabled.
+        '';
+      };
     };
   };
 
@@ -28,7 +40,7 @@ in {
       }
     ];
 
-    environment.systemPackages = [ pkgs.flatpak ];
+    environment.systemPackages = [ pkgs.flatpak ] ++ cfg.guiPackages;
 
     services.dbus.packages = [ pkgs.flatpak ];
 
diff --git a/nixos/modules/services/x11/desktop-managers/gnome3.nix b/nixos/modules/services/x11/desktop-managers/gnome3.nix
index 97eb74991abf..9dfac56c7fea 100644
--- a/nixos/modules/services/x11/desktop-managers/gnome3.nix
+++ b/nixos/modules/services/x11/desktop-managers/gnome3.nix
@@ -17,6 +17,11 @@ let
     '';
   };
 
+  defaultFavoriteAppsOverride = ''
+    [org.gnome.shell]
+    favorite-apps=[ 'org.gnome.Geary.desktop', 'org.gnome.Calendar.desktop', 'org.gnome.Music.desktop', 'org.gnome.Photos.desktop', 'org.gnome.Nautilus.desktop' ]
+  '';
+
   nixos-gsettings-desktop-schemas = let
     defaultPackages = with pkgs; [ gsettings-desktop-schemas gnome3.gnome-shell ];
   in
@@ -42,8 +47,7 @@ let
        [org.gnome.desktop.screensaver]
        picture-uri='file://${pkgs.nixos-artwork.wallpapers.simple-dark-gray-bottom.gnomeFilePath}'
 
-       [org.gnome.shell]
-       favorite-apps=[ 'org.gnome.Epiphany.desktop', 'org.gnome.Geary.desktop', 'org.gnome.Music.desktop', 'org.gnome.Photos.desktop', 'org.gnome.Nautilus.desktop', 'org.gnome.Software.desktop' ]
+       ${cfg.favoriteAppsOverride}
 
        ${cfg.extraGSettingsOverrides}
      EOF
@@ -123,6 +127,17 @@ in
         apply = list: list ++ [ pkgs.gnome3.gnome-shell pkgs.gnome3.gnome-shell-extensions ];
       };
 
+      favoriteAppsOverride = mkOption {
+        internal = true; # this is messy
+        default = defaultFavoriteAppsOverride;
+        type = types.lines;
+        example = literalExample ''
+          [org.gnome.shell]
+          favorite-apps=[ 'firefox.desktop', 'org.gnome.Calendar.desktop' ]
+        '';
+        description = "List of desktop files to put as favorite apps into gnome-shell. These need to be installed somehow globally.";
+      };
+
       extraGSettingsOverrides = mkOption {
         default = "";
         type = types.lines;
@@ -215,6 +230,11 @@ in
 
        # If gnome3 is installed, build vim for gtk3 too.
       nixpkgs.config.vim.gui = "gtk3";
+
+      # Install gnome-software if flatpak is enabled
+      services.flatpak.guiPackages = [
+        pkgs.gnome3.gnome-software
+      ];
     })
 
     (mkIf flashbackEnabled {
@@ -397,7 +417,6 @@ in
         gnome-music
         gnome-photos
         gnome-screenshot
-        gnome-software
         gnome-system-monitor
         gnome-weather
         nautilus