Mississippi College dropped to Division III at the end of 1995–96 and was replaced by Christian Brothers to keep the Conference at 16 schools.

Montevallo announced on June 27, 2008 that they would be leaving for the Peach Belt Conference following the 2008–09 season due to issues between the University's President and the Commissioner.

The next step in bolstering its membership came in 2012, backing the Division II application of Lee University (TN) which was on track to join the league officially in 2015-16.

The Conference planned to add an old friend back into the fold when Mississippi College submitted its application to rejoin Division II and was on track for 2016-17 membership.

The conference welcomed its seventh commissioner in May 2014 when Matt Wilson was selected to follow Nate Salant who retired after a 22-year stint.

[6] On October 11, 2012, Mississippi College announced that it would petition the NCAA to leave Division III and return to the conference.

Mississippi College entered its second candidacy year with the 2014-15 season in its path to full Division II membership in 2016-17 and added Gulf South Conference teams to its schedule.

[10] In May 2020, affiliate member Florida Tech announced the discontinuation of their football program due to the financial fallout of the COVID-19 pandemic.