[1] As a highly touted junior college prospect, Cooper chose to attend the University of Mississippi and play under head coach Hugh Freeze.
He made his debut on August 28, 2014, helping Ole Miss secure a 35–13 victory over Boise State.
Cooper chose to forgo the 2015 NFL draft and return to Ole Miss for his senior season.
He began the season as the starting left tackle after Tunsil was suspended 7 games for receiving improper benefits.
He started the season opener against UT Martin and helped the Rebels win 73–3 making it the most points they've scored since 1935.
Cooper was mid-season all-SEC by ESPN.com and won the Kent Hull Trophy as Mississippi's top collegiate offensive lineman.
[7] Going into training camp, Cooper was expected to compete for the 49ers' starting right guard position along with Ian Silberman and fellow rookies Joshua Garnett and John Theus.