Matthews was arrested over the weekend after an employee allegedly saw him abuse the dog and reported it. He is being charged with aggravated cruelty to an animal, a felony.
The dog's name is Montage, and the affidavit in this case says that Montage appeared to look normal after examined by a vet. Montage is being held at the Larimer Humane Society.
Matthews appeared for a short time in court Tuesday for an advisement hearing and would not comment on the case.
The affidavit, obtained by 9NEWS, paints a picture of the alleged incident.
The document says the employee captured photographs of a blood stained carpet, where Matthews allegedly beat the dog. It also says she saw Matthews slammed the dog's muzzled nose through some sheetrock in the office and body slammed the dog at least twice while holding its neck.
"I've never handled a case where the suspect has been a dog trainer, however I remind everyone that animal cruelty cuts across every kind of occupation," Diane Balkin, an attorney with the Animal Legal Defense Fund, said.
Matthews could face up to 18 months in prison and a $100,000 fine if convicted. A person commits aggravated cruelty to animals if he or she knowingly tortures, needlessly mutilated or needlessly kills an animal, Balkin said.
Matthews will be in court again on Friday.
Matthews is an Army veteran who specializes in training military and police canines.
"It's a very rare occurrence for us to pursue a felony charge, so we're taking this case very seriously," Marcie Willms with the Larimer Humane Society said.
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