The Crusaders held a 30-29 lead in the last seconds of the game but Zion responded with a field goal with just eight seconds left in the game.
The first quarter was a non-starter for the Crusaders as they struggled to find a spark and fell behind 12-4 to close out the quarter.
MCC slowly made up ground and trailed 20-14 at halftime and 24-18 to start the final quarter.
McKenna Gentry led the way for the Crusaders racking up 14 points on the night while Sara Albanese chipped in adding six points.
Muskegon Catholic Central falls to 8-10 on the season. The Crusaders are set to host West Michigan Christian in conference battle starting at 5:30 p.m. Friday.