Cal Poly's deepest football history predates its FCS era. Under Joe Harper (1968-1981), the Mustangs won 12 CCAA titles and the program's only national championship — a 21-13 win over Eastern Illinois in the 1980 NCAA Division II title game. Two Cal Poly alumni later reached the Pro Football Hall of Fame: John Madden, whose playing career at Cal Poly ended with a training-camp knee injury before he ever played in an NFL regular-season game, redirecting him toward the coaching and broadcasting career that defined him; and Bobby Beathard, Cal Poly's quarterback in the late 1950s, who spent four decades as an NFL personnel executive and built rosters that reached seven Super Bowls.

Cal Poly moved to Division I-AA (now FCS) in 1994 and joined the Big Sky Conference in 2012. Its clearest FCS-era peak came under Rich Ellerson (2001-2008, 56-34), whose tenure included a run matched only by Montana in FCS history: Cal Poly linebackers Jordan Beck (2004), Chris Gocong (2005), and Kyle Shotwell (2006) each won the Buck Buchanan Award as the nation's top defensive player in three consecutive seasons. Gocong's 23.5 sacks in 2005 remain an FCS single-season record.

Since Tim Walsh's 2016 team went 7-5 and reached the playoffs, Cal Poly has not posted a winning season. The program has cycled through three head coaches in six years — Beau Baldwin (4-21, 2020-2022) and Paul Wulff (10-24, 2023-2025, fired Nov. 23, 2025) — before hiring Tim Skipper, UCLA's interim head coach for the final nine games of 2025, to a five-year deal on December 3, 2025. Skipper inherits a program that just opened the $45 million John Madden Football Center in June 2026, a bet that new facilities plus new leadership can finally end the post-2016 drought.