In 1967, Cooper became defensive coordinator at Kansas under Pepper Rodgers. Cooper again was part of a conference championship team in 1968 when Kansas finished first in the Big 12. The 1968 Kansas team finished #9 in the final AP Poll and made the Orange Bowl. Cooper remained at Kansas until 1971. From 1972 to 1976, Cooper had his final assistant position at Kentucky, first under John Ray in 1972 then Fran Curci from 1973 to 1976. In Cooper's final season at Kentucky in 1976, Kentucky finished #18 in the AP Poll and won the Peach Bowl.