Amy Johnson, director of Puces POP, said about $25,000 worth of goods was stolen, along with the business cards of the artists targeted.
"It feels terrible — you don't think people are going to steal things made by artisans, made by hand, and you especially don't think they're going to do it in a church basement," she said.
Johnson said they locked up at Église Saint-Denis on Rivard Street on Friday night.
When they returned Saturday morning to open up for business, the doors were open and unlocked.
Montreal police believe either someone broke in overnight or hid inside as they closed up.
The triannual craft market has been a part of the pop music festival for 10 years. For this latest edition, 110 vendors took part.
Puces POP organizers believe the theft was planned and targeted, since the most popular vendors were hit. One had $11,000 worth of goods taken from her booth alone.
"We are thinking they are going to resell stuff as their own so we've contacted all the boutiques in Montreal that sell [the artists'] stuff," Johnson said.
The vendors were reimbursed their participation fee and POP Montreal is organizing a fundraiser to help them recoup some of the money.
"It will be a really small percentage of what they lost but it will be something"