The club joined the
Canadian Soccer League in 2018 with a team in the First Division.[3][4] The club was originally formed as an academy by
Krum Bibishkov.[5] Bibishkov would also serve as the head coach for the
2018 season.[6][7] Goalkeeper Senad Poračanin scored the opening goal in a 2–0 victory over
Brantford Galaxy on September 7, 2018, on a penalty kick.[8] They finished their debut season in seventh place in the nine-team league, qualifying for the playoffs.[9] Their playoff run ended in the first round of the postseason. where they were eliminated by
FC Vorkuta.[10] The club also provided free soccer workshops to students in
Dufferin-Peel Catholic District School Board schools.[11]
Bibishkov would continue as the head coach for the 2019 season.[12] Mississauga would fail to secure a playoff berth after finishing ninth in the divisional standings.[6] In the following season, the
COVID-19 pandemic delayed the commencement of the season and resulted in several teams opting out.[13] Initially, Mississauga was included in the delayed schedule but later the schedule was further delayed with the club not being included in the revised schedule.[13][14] Mississauga failed to return to the league after the pandemic with the club founder Bibishkov also leaving and returning to Bulgaria.[15]