It proved to be the final season for the West Virginia Intercollegiate Athletic Conference (WVIAC). Shortly before the start of the 2012–13 school year, the WVIAC's nine football-playing members announced plans to break away and form a new league. Before the new conference was announced, one of the nine breakaway schools (Seton Hill) chose instead to join the Pennsylvania State Athletic Conference; the remaining eight schools joined with three other football-playing schools and one non-football WVIAC member left out of the original split. The new league, officially unveiled in August 2012 as the Mountain East Conference, began play in 2013.
The GNAC, MIAA, and Great American moved from Super Region 4 to Super Region 3, while the RMAC and GLIAC moved in the opposite direction; the GLVC, newly sponsoring football, was assigned to Super Region 4.