Looking for a guide to help you install Mod Organizer 2 in Steam Deck? If yes, you have stumbled upon the right webpage.

Mod Organizer 2 is a well-known free and open-source mod manager. Unlike its predecessor, Mod Organizer, which primarily supported 32-bit games, it supports a wide range of games, including 32-bit and 64-bit games.

Some also consider Mod Organizer 2 as the predecessor of the popular Vortex Mod Manager because both tools come from the same developer, whose name is Tannin, but I have different opinions.

The reason is simple—the open-source community hasn’t abandoned the MO2 project, which is being actively developed; therefore, considering it a predecessor might be a vague statement.

Therefore, choosing it instead of any other mod manager wouldn’t be wrong. Since you’re interested in that, this article will help you install Mod Organizer 2 on your Steam Deck.

So, without any further ado, let’s get started –


Before installing MO2, complete these steps to ensure it installs correctly and does not create issues.

Essential Tools

Before installing any games on your Steam Deck, you need to make sure that the following tools are installed: Steamworks Common Redistributables, Steam Linux Runtime, and Proton 7.0 or above.

These tools are extremely important because they provide the necessary libraries and compatibility layers that many games require to run properly on Linux.

Check Compatibility

Although Mod Organizer 2 is compatible with a wide range of games, I recommend manually checking if it supports the games you want to mod. The list of supported games is here.

Install and launch the game.

I assume you have already installed the game on your Steam Deck. But if you haven’t, please do so, and then launch the game once in the game mode.

This is important for two reasons –

  • First, games like Skyrim and Oblivion require specific DirectX components for proper graphics functioning. When you run the game, it automatically installs and configures these components, preventing potential graphics-related issues arising after installing the Mod Organizer 2.
  • Second, MO2 and most other mod managers rely on specific directories to function properly. When you run the game for the first time, these folders get automatically created and configured, avoiding the chances of getting errors during the MO2 installation and modding process.

Install Protontricks

Make sure you have Protontricks installed on your Steam Deck.

If you don’t have it, head to Desktop mode. Then, search for the Protontricks on the Discovery Store and install the Flatpack version.

Next, open the Konsole Terminal and execute the following command –

echo “alias protontricks=’flatpak run com.github.Matoking.protontricks'” >> ~/.bashrc

Install Flatseal

Flatseal provides a range of benefits, but its most important feature is that it enables you to manage the permissions of all the Flatpak applications installed on your Steam Deck.

It also sends real-time alerts when updates are available to ensure that your Flatpak applications are always up-to-date. Once you have configured all of these settings, you can then install Mod Organizer 2.

Steps to install Mod Organizer 2 on Steam Deck

To install Mod Organizer 2  on Steam Deck, follow these simple steps –

  1. First of all, download the latest version of Mod Organizer 2. You can download it from MO2’s official website.
  2. Click on the downloaded MO2Installer.tar.gz file to open it. Note that the exact name may vary, depending on the version.
  3. Next, open the Dolphin file browser and navigate to the Downloads folder.
  4. Now, select all of the files inside the MO2Installer.tar.gz folder (the one we recently downloaded and opened) and drag and drop them into the Downloads folder.
  5. Next, close the MO2Installer.tar.gz folder.
  6. Now, head back to the Downloads folder and double-click on the install.sh file. It will open a dialog box, asking you to select your game. I am selecting Skyrim Special Edition for this tutorial, but you can select any other game.
  7. Select the game and click on the OK button. This will open a new dialog box, asking you to “clean your current game prefix before starting the installation process.” Select the No option.Although it recommends cleaning your current game prefix, you don’t have to do that. The reason is simple – we have Protontricks installed, and it keeps all the prefixes listed. Deleting the current game prefix will only cause issues with the MO2 installer, leading to unnecessary crashes and compatibility-related issues.
  8. Next, it will ask you to select the location where you want to install the Mod Organizer 2. Let everything set to default and click on the OK button.
  9. If it asks for any permissions or gives a warning, click on the OK button. It will then automatically start downloading and installing all necessary files.
  10. Once the installation is completed, you’ll receive a prompt stating, “Installation Successful!” Just click on the Continue button.

That’s it. You have successfully installed the Mod Organizer 2 on your Steam Deck.

How to use Mod Organizer 2

Now that you have installed Mod Organizer 2, check this step-by-step guide on mod installation using MO2 on Steam Deck –

  • The first thing you need to do is pick and download the mod you want to apply. To find mods, you can either join the game community and forums or head over to platforms like NexusMods and ModDB. In this tutorial, I am showing you how to apply a mod on Skyrim Special Edition, but the steps would be pretty much the same for any other game as well.
  • Next, open Steam and launch the game.If you have installed Mod Organizer 2 properly on your Steam Deck, the MO2 logo will pop up on your screen after launching the game, followed by the MO2 application.
  • Since you have launched MO2 for the first time, it will walk you through a step-by-step tutorial to help you learn the basics of the utility. Just play along with it, as it will make things easier for you.
  • Once you are in the MO2 dashboard, open the folder that contains the mod in a new window.
  • Next, drag and drop the mod file to the right side section of the MO2. Check the image shared below for reference.
  • Right-click on the mod you recently added to the Mod Organizer 2 and select the Install option.
  • A Quick Install dialog box will appear on your screen. Click on the OK button to install the mod.
  • Once the mod is installed, you can see it on the list on the left side. The unchecked mark before the name of the mod shows that the mod file is installed but not activated.
  • To activate this mod, right-click on it and then select the Enable selected option.
  • Once the mod is activated, select the Script Extender (SKSE in my case) and then click on the Run button to launch the game.
  • If everything goes right, you will see a pop-up on your screen stating, “Mods are currently loaded. Achievements are disabled. Do you wish to continue loading this save?”
    Just click on the Yes option to proceed.

Note that the exact warning message you will receive could vary depending on the game you’re modding, but it will mainly inform you about the changes in the mods.

That’s it. This is how you can easily install game mods using Mod Organizer 2.

Fix Directory Error

Many gamers have reported that MO2 throws an error when the game is installed on an external storage drive, such as an SD card.

Thankfully, this error is quite easy to resolve. All you need to do is follow these simple steps –

  • First of all, find the load_gameinfo.sh file. It will most likely be in the MO2INSTALLER-4_3_0/step/load_gameinfo.sh folder.
  • Open this load_gameinfo.sh file with a text editor of your choice.
  • At the bottom, you will see a defined variable named game_installation –
  • Here, you need to change the variable value to the location where your game folder is located. For example, in my case, Skyrim Special Edition is installed in this /run/media/SD/steamapps/common/Skyrim Special Edition location. Therefore, I have to change the variable value as follows –
    game_installation=”/run/media/SD/steamapps/common/Skyrim Special Edition”
  • After that, save the changes and execute the install.sh script again. This time, you won’t see any errors.

That’s it. This is how you can easily fix the directory-related error on Mod Organizer 2 in Steam Deck.

Additional Tips

You can follow the below-shared tips to get the most out of MO2 on your Steam Deck –

Keep Mods Updated

It is important to keep all mods updated in order to access new features and functionalities, improve system security, and ensure better compatibility with other mods.

Download Requirements

If you’re planning to use mods that significantly alter the game, like ENBs and overhaul mods, it’s important to carefully read their requirements to ensure they work properly. Once you have done that, you’ll need to download and configure all the necessary requirements on your Steam Deck.

Understand Limitations

Although you can technically install any mods on your Steam Deck, it is important to remember that it is not as powerful as a gaming PC. Therefore, it is recommended to exercise caution when installing heavy ENBs or overhaul mods, as these may cause the game to crash on your Steam Deck due to a lack of computational power.

Fix Clicking Issue

Several users have reported that they are unable to select any options within Mod Organizer 2. Although the root cause of this problem is unknown, a simple workaround is available that can resolve the issue immediately.

To resolve the problem, press and hold the Steam button located at the front of your Deck.

Final Words

There you have it – a detailed guide covering information on Mod Organizer 2.

Mod Organizer 2 is arguably the easiest and most user-friendly game modding solution, known for simplifying the game modding process. Despite that, modding is still a task and can potentially lead to unexpected behavior or instability.

Therefore, always approach modding cautiously, back up your saves regularly, and don’t hesitate to seek help from online communities if needed.

With that said, here I am wrapping up this article. I hope it was a helpful read for you.
If you have any questions, feel free to post them in the comment section below. Our team will try to respond as soon as possible.