So I found this out too when I couldn't get my controller to work in Battlefield. In order to get a ps4 controller to work on Origin, add your Origin application to Steam, then open up 'Big Picture Mode' and start origin through that, and then the controller will be recognized as an Xbox Controller.
Madden kept changing my Xbox one controller to keyboard.
This fixed the issue for me.
August 2018 - last edited August 2018
How do it ad them on steam ?
Go to Steam, the top left corner there is Games tab in tiny writing click that, then click add non-Steam game then scroll down to find Origin if not listed click browse to find origin in program files. Something like this C:\Program Files (x86)\Origin
Every time I launch madden, the "Set Active Controller" screen pops up. It recognizes my controller but continually pops up. I can mash A and move around the menu for about .25 seconds before it pops up again. Once I get into anything on the main menu the problem stops, until I am at the main menu again. this is driving me NUTS since I have had the game since a few days before official launch (deluxe edition).