Levi Hone claimed the Under 15 novice championship, while Liam Clohosey claimed the Under 17 novice championship.
Both were members of the college team that also included Logan Blachford and Martyn Currey.
The competition, which began in early June with a mountain bike race, saw competitors switch between mountain bikes and road bikes for a series of events.
The mountain bike sections of the event regularly included log rides, log jumps, rock sections, water crossing and copious amounts of mud, and two tracks - a more difficult "A track" to test out the riders, and a less challenging "B track" which was also known as the chicken track that would include less challenges, but take the riders longer.
Team coordinator Narelle Currey said she could not have been more proud of the team for their performances across the event.
“It really was a fantastic effort from everyone involved in our team,” she said.
“It was the first time they've competed in an event like this, they gave everything they had to be successful, the competed really strongly and came away with some fantastic results.”
Currey said the school's efforts to compete against bigger Melbourne schools made their achievements even more impressive.
“For a small school like ours to deliver two state champions was an exceptional effort,” she said.
“You take into account the people they raced against, students from really big schools across the state and into the city in Melbourne, people who are regularly competing in cycling events and competitions and have a lot of experience.
“For anyone to have success against competitors like that is impressive, but for these young riders in their first event to do that is something they can be very proud of.”