Head coach Mike MacIntyre resigned at the end of the regular season to take the head coach position at Colorado. Defensive coordinator Kent Baer was the Spartans' interim head coach for the Military Bowl. San Diego head coach Ron Caragher was hired as the Spartans new head coach beginning in 2013.
Head coach Mike MacIntyre returned for his third season with San Jose State. Under MacIntyre, San Jose State went 1-12 in its 2010 season and improved to 5-7 in 2011.
On December 10, the University of Colorado at Boulder hired MacIntyre to be the new head coach of the Colorado Buffaloes football team. With a five-year, $10 million contract, MacIntyre would annually earn nearly quadruple his annual salary at San Jose State. The following day, San Jose State named defensive coordinator Kent Baer to be interim coach for the 2012 Military Bowl on December 27, in which they defeated Bowling Green 29-20. The previous week, MacIntyre stated that although other schools had contacted him about potential job openings, MacIntyre was not actively seeking another job. During San Jose State's late-season win streak, speculation occurred that MacIntyre might become head coach at Cal or Kentucky in 2013.
On November 3, San Jose State became bowl eligible for the first time since 2008 after beating Idaho and attaining six wins against FBS schools. However, the win over UTSA did not count, because UTSA was not yet a full FBS member school.
Six games were nationally televised this season. ESPN showed the Military Bowl on December 27, ESPN2 showed the games against BYU and Louisiana Tech, CBS Sports Network showed the game against Navy, and Pac-12 Network showed the game against Stanford.WatchESPN also streamed the games shown on ESPN and ESPN2 as well as two games—the ones against Colorado State and UTSA—broadcast by ESPN3, the game against New Mexico State via New Mexico State's AggieVision network, and the game against Utah State via ESPN Regional Television.
KLIV in San Jose served as the flagship station for the San Jose State Spartans Football Radio Network, along with fellow affiliates KION in Salinas and newcomer KFIV in Modesto. Michael Spero returned for his second season as play-by-play announcer, with Kevin Richardson at color commentary.
Scoring for Stanford: S. Taylor 1-yard run, J. Nunes' 11-yard pass to D. Terrell, J. Williamson 46-yard and 20-yard field goal. Scoring for San Jose State: Austin Lopez 38-yard field goal, Blake Jurich 3-yard run, and David Fales' 21-yard pass to Noel Grigsby.
In San Jose State's homecoming game, San Jose State lost to eventual WAC champion Utah State. Although David Fales completed 38 of 50 passes for 467 yards and three touchdowns, Fales was sacked 13 times with a cumulative loss of 102 yards. Utah State also had a 212-4 advantage in rushing yards.
Travis Johnson earned the WAC Defensive Player of the Year award. With 16 honorees, San Jose State led all WAC teams in 2012 for All-WAC honors. Named to the All-WAC first team were Noel Grigsby, Ryan Otten, Nicholas Kaspar, David Quessenberry, Travis Johnson, Travis Raciti, Vince Buhagiar, Keith Smith, and Bené Benwikere. Named to the All-WAC second team were Chandler Jones, David Fales, De'Leon Eskridge, Anthony Larceval, David Tuitupou, Austin Lopez, and Tyler Ervin.
On July 1, 2013, San Jose State officially became a member of the Mountain West Conference (MWC). San Jose State football followed fellow WAC school Utah State to the MWC and reunited with Hawaii in football only and Boise State, Fresno State, Nevada, and several other fellow former WAC schools in football and many other sports. The WAC stopped sponsoring football after the 2012 season.