Upon ending his playing career, Clemons became interim head coach of the Toronto Argonauts in 2000, replacing John Huard, who resigned after compiling a 1–6–1 record. When offered the head coaching job by team general manager J. I. Albrecht, Clemons was reluctant to accept it, wanting to spend more time with his family. According to Clemons, "it was an awkward situation. After saying no, they said do us the favour of going home and discussing it with your family. The burden was that this team, this organization, had given our family so much that Canada was going to be our home. The Argos had everything to do with my family becoming a part of this country. Because of all I had been given I decided it was my time to reciprocate." As interim head coach, Clemons coached the Argos to 6 wins out of their remaining 8 games. He had the interim tag removed from his title at the end of the season. In November 2001, he was promoted to President of the Argonauts and relinquished his role as head coach in the process to Gary Etcheverry.