Officials at the Kingsway Baptist Church at Bloor Street and Royal York Road say their building was left in shambles.
Someone broke in at about 3:30 a.m. on Friday, tearing up Bibles and causing widespread damage.
"Throwing paint and discharging the fire extinguishers everywhere," said Pastor Wayne Dickau. "Sanctuary, the kids' rooms, all the various program areas, seems like there wasn't a room that was left untouched."
A security guard called police once the alarm had been triggered.
The suspect is thought to have hopped a fence and run in the direction of Mimico Creek.
Police said the suspect likely has paint on the soles of his or her shoes.