Mahomes began the 2007 season with the Sioux Falls Canaries of the American Association. On August 24, the Toronto Blue Jays signed him, and he appeared in three games for the Syracuse Chiefs before becoming a free agent at the end of the season. Mahomes signed with the Southern Maryland Blue Crabs of the Atlantic League in , but only appeared in two games for them before returning to Sioux Falls. He split the 2009 season between Sioux Falls and Grand Prairie.