Following his playing career at Missouri State University, Spavital became a member of the coaching staff at Tulsa in 2008 where he worked as an offensive quality control assistant under Gus Malzahn. Following the 2008 season Spavital became a graduate assistant at Houston. While at Houston, Spavital worked under head coach Kevin Sumlin and offensive coordinator Dana Holgorsen. Spavital became familiar with Holgorsen's offense while working at Houston, and when Holgorsen became the offensive coordinator at Oklahoma State in 2010 he took Spavital with him and gave him the same position of graduate assistant. Spavital was an essential piece of Holgorsen's coaching staff at Oklahoma State because he was the only person on the staff familiar with the offense that Holgorsen ran. Spavital helped teach the new offense to QB Brandon Weeden, who was nearly two years older than Spavital. That season, Oklahoma State went 11-2 and Weeden was third in the nation in yards per game and total yards as well as sixth in the nation in touchdowns. When Holgorsen became head coach at West Virginia before the 2011 season, he took Spavital with him and made him quarterbacks coach. While at West Virginia, Spavital coached Geno Smith. Under Spavital's coaching Smith would break numerous WVU, NCAA, and bowl records. When Texas A&M offensive coordinator Kliff Kingsbury left Texas A&M to become the head coach at Texas Tech, A&M head coach Kevin Sumlin offered Spavital the position. At Texas A&M, Spavital started as the co-offensive coordinator with Clarence McKinney and was the quarterbacks coach. In the 2013 season, he coached Heisman Trophy winner Johnny Manziel. On January 3, 2016 Spavital and Texas A&M mutually parted ways, partially in lieu of the Kyler Murray/Kyle Allen quarterback controversy during the 2015 season that saw both highly rated QBs transfer out of A&M the same season. On February 11, 2016 Spavital was announced as the offensive coordinator and quarterbacks coach for the California Golden Bears football team. On January 8, 2017, following the firing of head coach Sonny Dykes, it was announced that Spavital would serve as interim head coach at Cal. On January 13, 2017 it was announced that Spavital would be returning to West Virginia as offensive coordinator, rejoining Holgorsen and offensive line coach Joe Wickline, who he coached with while with Holgorsen at Oklahoma State.
On August 29, 2019 Spavital and Texas State lost to No. 12 ranked Texas A&M 41-7 in Spavital's first game as head coach. On September 21, Spavital recorded his first win as a head coach when his Bobcats defeated Georgia State, 37-34, in 3 OTs.
