Following graduation both brothers joined Kindbom's coaching staff; their paths finally diverged in 1999 when John departed the coaching staff to attend the
University of Missouri School of Law. He entered private practice and died in 2019 at the early age of 47. Aaron Keen's first role on the coaching staff was tight ends coach for the 1994 season. He remained on the staff through the end of the 2002 season, spending the last four as
offensive coordinator. In early 2003 he departed Washington University to become head coach at
Illinois College in
Jacksonville, Illinois, replacing
Tom Rowland.
Illinois College and Nebraska–Omaha Illinois College, a Division III school like Washington University, competed in the
Midwest Conference. Keen retained much of Rowland's staff; one noteworthy hire was defensive coordinator
Jim Ryan, who had held the same position at
Colorado College. In five seasons Keen compiled an overall record of 23–27; the team's best finish was 4th in conference play in 2004 and 2006. Keen departed Illinois after the 2008 season to become offensive coordinator at the
University of Nebraska Omaha, replacing
Terrence Samuel. His replacement at Illinois was
Garrett Campbell, formerly offensive coordinator at
Carthage College in
Kenosha, Wisconsin. The University of Nebraska Omaha (UNO), under long-time head coach
Pat Behrns, was coming off three consecutive appearances in the
NCAA Division II Football Championship, making it to the second round each time. After the 2007 season the school changed conferences, moving from the
North Central Conference to the more competitive
Mid-America Intercollegiate Athletics Association (MIAA). The move to UNO reunited him with Brad McCaslin, who had been on the staff there since 1997 and
defensive coordinator from 2005. Keen and McCaslin found themselves suddenly out of a job in the spring of 2011 when UNO decided to transition to
NCAA Division I and join the
Summit League. As part of this change, UNO dropped football and wrestling.
Minnesota State Keen landed on his feet, taking over as
offensive coordinator at
Minnesota State University, Mankato in
Mankato, Minnesota, under head coach
Todd Hoffner. Minnesota State competed in the NCAA Division II
Northern Sun Intercollegiate Conference. Keen found himself thrust into an unusual and difficult situation in 2012, when Hoffner was charged with possessing
child pornography and suspended from his duties. Hoffner was eventually exonerated and returned to his position for the 2014 season, but Keen acted as head coach for the 2012 and 2013 seasons. In his first season Keen led Minnesota State to a 13–1 record and an appearance in the NCAA Division II Football Championship, making it all the way to the semifinals. Minnesota State changed his title from "acting" to "interim" head coach. In 2013 Minnesota State went 11–1, again winning its conference and earning a place in the championship, though it lost in the second round. Minnesota State reinstated Hoffner in early 2014, leading to a brief revolt by the players who objected to the supersession of Keen. Hoffner met with the players and the question of his return was resolved amicably, but Keen departed two weeks later to become the special teams coordinator and tight ends coach at
Eastern Michigan University.
Eastern Michigan The move to Eastern Michigan again reunited him with McCaslin, who had followed new head coach
Chris Creighton from
Drake University after the 2013 season. Eastern Michigan, located in
Ypsilanti, Michigan, competed in the
Mid-American Conference of the
NCAA Division I Football Bowl Subdivision. Eastern's defense struggled, and McCaslin was fired after the 2015 season. Creighton promoted to Keen to offensive coordinator in 2017 after
Kalen DeBoer departed to become offensive coordinator at
Fresno State. Keen's tenure at Eastern Michigan was successful, and after the 2019 season he departed to become a head coach again–at Washington University, his alma mater.
Washington University At Washington University, Keen's former head coach Larry Kindbom was retiring after 31 years. The two men had remained close; when John Keen died in 2019 Kindbom took on the job of communicating the news to Aaron and John's former teammates. Washington University now competed as an affiliate member of the
College Conference of Illinois and Wisconsin, still within Division III. The
COVID-19 pandemic led to Washington University suspending fall sports for the 2020 year, delaying Keen's coaching debut there. ==Head coaching record==