He also coached at his alma mater, Texas State University, where he led the Bobcats to the NCAA Division I-AA National Semifinals in 2005.

[1] On February 5, 2004, Bailiff again returned to his alma mater, which by now was known as Texas State University, this time as head coach.

They then won two games in the NCAA Division I-AA playoffs, eventually losing to Northern Iowa.

On January 19, 2007, Rice University hired Bailiff as head coach, replacing Todd Graham.

The Owls won that game 38–14 for Rice's first 10-win season since 1949, and Bailiff was rewarded with a five-year contract extension.

Unlike his previous tenures at Rice and Texas State, Bailiff was taking over an A&M-Commerce program that had deep tradition and that was considered by most Division II football observers to be the best Division II program in Texas.

In his first season at Texas A&M-Commerce, he led the Lions to an 11-3 record, finishing 2nd in the Lone Star Conference.

In the second round, they defeated Rocky Mountain Athletic Conference Champion and previously undefeated Colorado School of Mines 23-3 to send them back to the Region 4 Championship for the second time in 3 years.