The Nairobi-based side had just handed a walkover to Gor Mahia on Thursday after the players refused to play, demanding for unpaid salaries to be paid.
Despite the shambolic preparations, the Melis Medo-led side gave their best on the pitch to claim maximum points. After settling early and pinning their opponents in their own half, the visitors lacked composure in front of goal.
When it seemed that the first half would end goalless, Norman Werunga capitalised on a defensive lapse to score for his team in the 44th minute.
Mount Kenya doubled their advantage in the 68th minute, courtesy of former Mathare United striker Brian Nyakan.
The hosts had to do something to get into the match and after missing some good chances, Derrick Anami halved the deficit with a good header after the defenders failed to clear the danger.
That goal did little to affect the inspired Mt. Kenya side and a few moments later, Brian Nyakan completed his double to put the game beyond the home side.
Danson Chetambe scored late into the game to give Zoo a second goal but that was too little too late as the visitors held on to bag crucial points.