In their first four years of existence, the Koyotes dominated the APFL. They went undefeated in the 2003 and 2004 seasons, beating the Missouri Minutemen in the championship game both times.

In the 2005 season, they went undefeated again, albeit being in many close games, winning their third championship over the Iowa Blackhawks by a field goal kicked as time expired.The winning streak lasted 31 games, including exhibition games and post-season games.

2006 is when the Koyotes finally met their Waterloo in Wichita, losing to the Wichita Aviators in the season opener.They would lose to the Aviators again, and finish second in the regular-season standings to the Aves. The two teams were going to play for the APFL Championship at the Wichita Ice Arena, for reasons that may never be clear, the league moved the game to Landon Arena. There was never a true explanation offered for this decision, and the game never took place.

In 2007, the Koyotes continued their domination by winning all their regular season home games and losing only two road games. They proceeded to win the championship game against Iowa Blackhawks. During the season the Koyotes signed Abby Vestal as their kicker. On April 23, Vestal kicks three PATs becoming the first woman to score points in a professional men's football game. Vestal, who signed a soccer scholarship for 2007 with Johnson County Community College in Overland Park, Kansas, would kick 6-9 PATs and go 0-2 in FGs.

Starting with the 2013 season, the Koyotes joined the Champions Professional Indoor Football League for two years.

Focusing on bringing a total entertainment venue to northeast Kansas, the Koyotes announced after the 2014 Season ended that they would leave the CPIFL and play 2015 as an independent, increasing to 8 home games.