Jean-Luc Rodier is facing charges related to 90 foxes, 10,000 mink and two dogs held captive in his St-Jude, Que., facility, south of Montreal in the province's Montérégie region.
The animals were photographed and filmed during a criminal investigation conducted by the Montreal Society for the Protection of Animals (SPCA) in May.
The SPCA is responsible for investigating allegations of animal abuse in Quebec.
SPCA director of animal advocacy Alanna Devine told CBC News in August that she was horrified when she arrived at the farm.
"Animals not having access to adequate water, large amounts of excrement, filthy cages … the sort of things that would be outrageous if we saw dogs… wired bottom cages, no access to a solid floor," said Devine. "Difficult things to see."
Rodier is due back in court April 13.
He could face up to 18 months in jail and $10,000 in fines for each count, as well as a lifetime ban on having an animal in his custody or under his control.