Quit Emulationstation by pressing your menu button (on the controller), going to quit, then select “Exit Emulationstation”.

Then type the following (CASE SENSITIVE!). Press Enter after each line.

sudo chown pi /opt/retropie/configs/all/retroarch.cfg

cd /opt/retropie/emulators/RetroArch/installdir/bin

sudo ./retroarch-joyconfig -j 0 >> /opt/retropie/configs/all/retroarch.cfg

The last command will launch a controller configuration tool. You have to input the buttons pretty quickly! If you make a mistake, after going through the program, press up to input the previous command.

Once you’re happy with the setup, reboot, or type:

emulationstation

Then load a game and see if it works. This affects every emulator that uses the Retroarch cores. MAME and Gameboy Advance have their own internal methods of assigning controls.

You can tweak the control scheme manually as well. Connect to the Pi and edit the following file: /opt/retropie/configs/all/retroarch.cfg