Baker fell to 6-4 and 0-1 in the HAAC, while MidAmerica Nazarene improves to 7-1, 1-0 in the conference in both teams conference openers.
Brianna Garza led the Wildcats with 17 points, while Shea Shoemaker and Kyrstie Ehm also scored in double figures with Shoemaker totaling 15 points, while Ehm scored 11.
The Pioneers outrebounded the Wildcats 43-34 and Kelsey Balcom led MidAmerica Nazarene with 13 points and two rebounds and Kyleesha Weston led the team with seven rebounds.
Baker led by 10 with 13:22 left in the first half, but gave up the lead quickly and trailed 46-39 at halftime.
The Pioneers had an astounding 36 bench points compared to just 11 by BU and had 17 points off turnovers.
The Wildcats were an uncharacteristic 5-of-15 from beyond the arc and 2-of-9 in the second half.
MidAmerica Nazarene shot 87 percent from the charity stripe, while Baker was 83 percent.
The Wildcats will next travel to Lamoni, Iowa to face Graceland on December 14 at 2 p.m.