	Cooper eventually returned to competition, but had another injury setback in 1993, when he pulled a groin and missed three months of rodeos. Later that year, he won all-around and steer roping championships at Cheyenne Frontier Days. In 1994, he was out of action for much of the year after rotator cuff surgeries. He claimed a calf roping title at the 1995 San Antonio Stock Show & Rodeo. Later in the year he had the fastest average calf roping time at the NFR, which was later described as Cooper's "favorite moment" at the event. Cooper finished second in the All-Around Cowboy standings in 1996. That year, he led the NFSR in average earnings in steer roping; Cooper became the first cowboy to win four NFR average steer roping titles, a record that has since been surpassed by Guy Allen. It was the eighth NFR average title of his career and his ninth overall NFR championship, counting his 1983 all-around victory. As of 2016, he was second among cowboys in NFR titles, behind Trevor Brazile, and first with all-around championships excluded. At a 2000 rodeo in Lovington, New Mexico, he surpassed $2 million in earnings; Cooper was the first to reach this mark in rodeo. As of 2011, Cooper remained a part-time competitor in rodeo events. By 2016, he had retired.