• Download Mod Organizer 2 (the Archive version) manually from the Nexus.
  • Extract the archive to a new folder on the same hard drive as your Skyrim SE installation, outside the UAC protected folders.
  • Run ModOrganizer.exe.
  • A window will come up – select Portable.
  • Next you will be asked which game to set MO2 up for. Normally it should recognise your Skyrim SE installation automatically.
  • Select Skyrim Special Edition in the list.
  • Confirm when asked to associate NXM links with MO2.
  • Click No when prompted with the tutorial option.

Note: Installing MO2 with a portable instance means all of its subdirectories will be located inside the MO2 root folder which is required for some modding tools to work properly.


  • Open the Settings (Tools > Settings or CTRL + S).
  • Switch to the Nexus tab where you need to connect your Nexus account to Mod Organizer 2.
  • Click Connect to Nexus.
  • This will open a Browser window where you will be asked to confirm.
  • Click Authorise. You can revoke this any time in your Nexus settings.
  • Mod Organizer 2 may ask you to restart. Click OK.


Most people use the “With Mod Manager” download option on the Nexus and then install the mod through their mod manager’s UI. That is the fastest and simplest way to download and install mods which is why we already set up MO2 for it.

Since we installed MO2 as a portable application, all our mod archives would normally be downloaded into a sub-directory of the (MO2) root folder – which in turn may be located on your SSD or otherwise fastest hard drive. These archives are then extracted into their own folders meaning after their installation they only use up space. However keeping the archives as backups is necessary as mods are occasionally taken down from the Nexus or in case something goes wrong during the installation.

Here is where our ARCHIVE comes into play, the directory inside Your Modding Folder we set up to store all the mod files on a hard drive with plenty of free space. We will now configure Mod Organizer 2 to save all downloads to that folder.

  • Once again, open the Settings in MO2.
  • Switch to the Paths tab.
  • Point Downloads to Your Modding Folder\ARCHIVE\MO2 Downloads.


You can now configure the UI to your liking. Personally I re-arrange the two panels so that the left one (mod order) is wider.

  • Right-click the Tool Bar (where you can see the coloured icons in the top left).
  • Now you may choose which parts of the UI to display. I recommend disabling Log and Status Bar as you won’t need either.
  • For the main Tool Bar you can decide between Icons or Text (or both), and, if you choose Icons, their size. This is up to you.

Note: I personally disable to Tool Bar altogether as I can access everything through other menus or shortcuts but for beginners it may be preferable to keep it enabled.


If it’s the middle of the night and you prefer dark mode to go easy on your eyes, open the Settings (CTRL + S) and choose a different theme under Styles. Paper Black Mono or Paper Dark are the obvious choices but there are more options.


Open the Settings (CTRL + S) and check both boxes in the General > Download List section. This will make it easier to navigate your downloads, see more of them at a glance and tell different files apart.


By right-clicking the top of the left pane, you can choose what to display in your mod order. Enable the following columns:

  • Conflicts
  • Flags
  • Content
  • Version
  • Source Game
  • Priority

Click on the picture to below to open it in full size.


  • Open the Profile settings in MO2 by clicking the ID card icon in the top left icon bar.
  • Click Create and enter The Phoenix Flavour as name.
  • Default Game Settings should be unchecked. Click OK to confirm.
  • Select your new profile in the list.
  • Check both Use profile-specific Save Games and Use profile-specific Game INI Files.
  • Click Close to exit the settings.
  • In the profile list below the top left icon bar in MO2, select your new profile to switch to it.

Profile-specific Save Games
MO2 can allow Skyrim SE to only load saves created with the profile you are currently on. This is quite useful to separate different playthroughs from each other as well as from test characters and saves.

Profile-specific INIs
MO2 is capable of handling the INI files (Skyrim.ini and SkyrimPrefs.ini) separately and attach them to a profile. This way the original INI files in the INI folder remain entirely untouched plus you can manage multiple different setups in MO2 each with their own set of INIs.


  • Download the The Phoenix Flavour – MO2 Separator Pack manually from the Nexus.
  • Open the downloaded archive.
  • Extract all folders ending on _separator to Mod Organizer 2\mods.
  • Switch back to Mod Organizer 2 and press F5 to refresh. The new separators will now appear in your mod order.
  • They are numbered so simply put them in the correct order (and use the opportunity to move DLC: Dawnguard above DLC: HearthFires):
    • DLC: Dawnguard
    • DLC: HearthFires
    • DLC: Dragonborn


Managing the plugins of mods included in a merge in a way that allows you to recreate the merge at any time can be a little annoying. Fortunately there is a plugin by Deorder to hide and unhide those plugins at any time directly through the MO2 UI.

Note: There is a second plugin in deorder’s bundle, Sync Mod Order, which used to be incredibly convenient but hasn’t worked properly (for me) since the 2.0+ versions of Mod Organizer 2.

  • Open the Github page for deorder’s MO2 Plugins.
  • Click the Clone or download button and select Download ZIP.
  • Open the downloaded archive.
  • Navigate to Mod Organizer 2\plugins.
  • Extract the following folder and files from the archive into the plugins folder:
    • data
    • .editorconfig
  • Confirm when asked to merge the data folders.


This step is optional and written for beginners who never used MO2 before.

Mod Organizer has a reputation for coming with a steep learning curve and that is true to an extent. Fortunately the UI is quite straight-forward and you are not required to know about all its tricks and features just yet. Knowing how to navigate the general layout, how to access its menus and what the different panes and tabs are about will however help you greatly in following this guide.

At present I recommend mnikjom’s quickstart introduction to MO2 which covers all the information necessary with short descriptions and screenshots. It is an article and part of his YASHED guide. You can read it here.

Alternatively, there is a brilliant and up-to-date series of video guides by GamerPoets on YouTube – How to use Mod Organizer 2. You can skip the first video (covering Installation & Setup) but do take a look at his video on Mods & Mod Management (linked below). The remaining three are also of great quality and very helpful but you don’t necessarily have to watch them in order be able to follow this guide.

There will be a brief tutorial on MO2 specifically written for The Phoenix Flavour at some point in the future.

Note: Yes, I am aware that the video below has been replaced by a newer one but this one is more comprehensive.