Shirley is accused of kicking and stomping Mark Daniel Haines after a December 2010 police chase and falsifying records during a subsequent investigation.
Haines is serving a 19-year sentence for bank robbery. Court documents say he suffered scrapes and bruises on his face and back during the beating, as well as a hemorrhage in his right eye, and a broken nose, rib and eye socket.
A separate civil lawsuit stemming from the alleged assault is scheduled for trial this fall.
Prosecutors in the criminal case also said they planned to introduce two video recordings from May 30, 2012, that show Shirley and another uniformed officer in what appears to be a booking room. The nature of the discussion on one video was not revealed, but prosecutors said the other had no audio.
The transcript, meanwhile, was from a sentencing hearing that former U.S. District Judge Craig Broadwater was holding in a separate case.
Shirley, then a lieutenant with 23 years of service, was testifying for the prosecution when he was questioned about his dealings with a man named Scott Rind over a piece of furniture that Rind had allegedly refinished and sold, knowing it belonged to Shirley.
Shirley testified that his wife, Debbie, had cheated on him with Rind years earlier.
"I was working one day, and I drove up on them and caught them in the act," he testified. "I shot at him one time, and that was it."
An attorney then asked if he typically shoots people who are sleeping with his wife while he's on duty.
"Well, I had never been faced with that before, but I did that time," Shirley responded. "I don't typically, no."
Shirley and his wife later divorced.