He was selected by the San Francisco 49ers in the third round of the 2009 NFL draft and played one season before retiring from football in 2010 and serving in the U.S. Army from 2013 to 2017.

In Alabama's homecoming game versus Utah State, he scored his first collegiate touchdown on a 9–yard reception from quarterback John Parker Wilson.

[5] In the 2008 season, Coffee was the starter in all 14 games, though he shared time with two other running backs, Roy Upchurch and Mark Ingram II.

[12] Coffee's career best game came in the following week in a 17–14 win over Kentucky, as he ran for 218 yards on 25 attempts, including a 78-yard touchdown run in the first quarter.

[14] Alabama clinched a berth in the 2008 SEC Championship Game with a 27–21 overtime victory over LSU, in which Coffee rushed for 126 yards and one touchdown.

[16] After rushing for 112 yards in the SEC Championship game loss to Florida,[17] Coffee was held to his season low in the 2009 Sugar Bowl against Utah.

[24] After attending OTAs minicamp, and two weeks of training camp, Coffee abruptly announced on August 13 that he would retire just before the start of the 2010 NFL preseason.

[25][26] Head coach Mike Singletary stated that sixth round draft pick Anthony Dixon and veteran Michael Robinson would compete for the second running back spot and that Coffee's departure would not be a distraction to the team.

However, on August 16, the 49ers signed free agent veteran Brian Westbrook as the backup running back to a one-year deal.

[28] On April 21, 2017, Coffee was officially reinstated by the NFL and was subsequently released by the San Francisco 49ers who still owned his player rights.