The Wildcats fell in its fourth straight conference game and now stand at 14-12 overall and 7-9 in the Heart of America Athletic Conference.
MNU improved to 20-7 overall and 12-3 in the HAAC and have won three straight conference games.
Ben Steinlage was stellar for the Wildcats with his game high 24 points on 7-of-14 shooting from the floor and 9-of-12 from the free throw line.
The Pioneers dominated the boards, outrebounding Baker 41-29 and Brandon Newton had a double-double with his 15 points and 12 rebounds.
MNU had three scorers in double figures, as Rustin Dowd added 15 and Nick Syrie had 10.
Baker had just one lead on the day when Corey Anderson started off the game with a basket to put Baker up 2-0, but MNU took over from there and led throughout.
The Wildcats will take on Benedictine College on Thursday, Feb. 21 at 7:30 p.m. on Senior Night at the Collins Center.