The agency believes the 36 cats and 57 dogs were living in what it describes as dangerously unhealthy conditions.
"[They were] really deplorable conditions. We're obviously still building our file but there are a lot of medical issues, things related to animals being kept in close confinement, exposure with ammonia and just lack of general care," said Alanna Devine, director of animal advocacy at the Montreal SPCA.
Devine said that means the animals could have been cooped up in small cages, in their own excrement and urine.
The animal protection agency won’t reveal the name of the facility, but it says it has been building a case against the breeder for some time.
It suspected the breeder was violating conditions of the province's animal protection act.
The SPCA is currently working on the case to see if the breeder can face charges.
The breeder could face a maximum $12,000 fine per charge or be permanently banned from running a breeding facility.
The rescued pets are now under veterinary care and the SPCA believes the animals were intended to be sold in pet stores or online.
"The fact that [mass breeders] continue to exist is fact or signal for us that we need stronger legislation. We feel that everybody breeding animals for commercial purposes should be required to get a permit," said Devine.
Right now there's a permit system for facilities that have 15 animals or more.
Devine wants the cap on the maximum number of breeding animals to be lowered.
She says the best way to prevent illegal breeding is to adopt pets, rather than purchase them from stores or breeders.