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emphyrio: EDIT:

Controller didn't work under linux, solved the problem.

For controller support to work in linux you may need to add this game to your steam library and start it from there. No need to buy it at steam, just add it as a non-steam game and start it from the steam interface.
Hey emphyrio,

This is most likely this issue:

The solution is described in the wiki - if your controller is not recognised by Owlboy you should drop a 'gamecontrollerdb.txt' file in the game folder and if your controller config is on the list, that will solve the issue. This file can be downloaded from here:

Sorry for the delayed answer.