In 2004, Beebe began coaching football for Aurora Christian Schools in Aurora, Illinois. He—along with his brother, defensive coordinator David Beebe, and brother Dan, the school's athletic director—led the Eagles to the school's first state championship appearance in 2008, where the team finished as 4A state runner-up after losing to Bloomington Central Catholic 37–28. Three years later Beebe and the Eagles returned to the finals, this time winning the 2011 IHSA Class 3A State Championship with a 34–7 win over Mt. Carmel. In 2012, Beebe led the Eagles to a second straight IHSA Class 3A State Championship by defeating Tolono-Unity 42–12 before stepping down as coach after the 2013 season and an overall 97–26 record. His brother succeeded him as head coach.