In 2000, Conlon was named the first full-time soccer coach in Wartburg College history and coached both the men's and women's soccer teams. During his time coaching the men's team, he led them to 5 straight NCAA tournament appearances and posted a record of 108–48–10. On the women's side he led them to the 2007 IIAC title and to the schools first ever NCAA tournament berth. He was named IIAC Coach of the Year on two occasions in 2003 and 2004.
Following a one-year absence, Conlon returned to Washington University as head coach of the women's soccer program. He led them back to the NCAA title game just two years after his return and then won the programs 2nd national title in 2024, Conlan's 3rd of his career.