The fire began in a trailer at the back of the building that was being used for storage, but quickly spread to the roof of the main repair shop.
Firefighters needed about an hour to put out the fire and nobody was injured.
Montreal police are now investigating and said clues found at the scene suggest the fire was intentionally set.
A man was arrested near the scene and will be questioned today by police.
The damage was estimated at just over $ 15,000.
Founded in 1995, SOS Vélo is a not-for-profit group that builds and re-sells bicycles to help adults re-integrate into the workplace.
The organization only hires candidates aged between 18-55 and who didn’t complete high school.