It happened in the area of Stevenson Street and Speedvale Avenue at around 9:30 p.m.
Police said there was an argument between two groups inside an apartment unit that led to a 24-year-old man getting shot in the thigh.
A suspect and another man fled the residence in a black SUV, while the victim was taken to hospital with non-life-threatening injuries.
The black SUV was spotted by officers in the downtown core on Monday and a 29-year-old man was arrested when he returned to the vehicle.
Police said they found a loaded semi-automatic pistol, ammunition and crystal meth.
The Guelph man faces several charges, including assault with a weapon and several firearm-related offences.
Guelph police are still trying to track down the other man who left the scene of the shooting in the SUV. They say he is considered at witness in the investigation.
Anyone with information is asked to contact the lead investigator at 519-824-1212 ext. 7202.
Anonymous information can be left with Crime Stoppers 1-800-22-8477 or through their website.