Until 1997, Limestone competed for championships in the National Association of Intercollegiate Athletics. Limestone gained membership in the National Collegiate Athletic Association'sDivision II in 1991 and began competing for NCAA championships when it joined the Carolinas-Virginia Athletics Conference in 1998. Today, 17 of Limestone's athletic teams compete in the Conference Carolinas, while both swimming teams are affiliated with the Bluegrass Mountain Conference. In 2014, the field hockey team joined the inaugural ECAC Division II conference in that sport and was joined by wrestling for the 2015–2016 season. Limestone helped pave the way for collegiate lacrosse, swimming, and field hockey in the South. The Saints fielded South Carolina's first collegiate lacrosse team in 1990. The swimming teams are the only NCAA Division II swimming programs in South Carolina and among the few in the two Carolinas. Over the years, the Saints baseball, men's and women's basketball, men's and women's golf, men's and women's lacrosse, softball, men's soccer, wrestling, and men's and women's tennis teams have all been ranked on the national level. Twelve student-athletes have gone on to play professionally in their sport, with seven of those signing professional baseball contracts. The Saints baseball program was started by two-time Cy Young Award winner Gaylord Perry, a member of the Major League Baseball Hall of Fame. Additionally, Saints athletes have earned All-American honors on over 100 occasions and over a dozen have been named Academic All-Americans.
Limestone is an established powerhouse in men's lacrosse and has won five national championship titles. The Saints have also compiled nineteen Conference Championship titles in. With its 2000 national title, Limestone College became the smallest coeducational institution to ever win an NCAA national championship. They are set to play on Sunday, May 26, 2019.
Women's lacrosse
The Limestone College women's lacrosse program has made appearances in nine NCAA Division II National Tournaments, reaching the NCAA DII National Championship in both 2011 and 2013. They have been regular-season conference champions for thirteen consecutive seasons and accumulated nine conference tournament championships. They are the southern-most collegiate women's lacrosse program to make an appearance in a national tournament. The current Head Coach of the program is Scott Tucker. Tucker beginning in 2015 became the winningest active coach in NCAA Division II women's lacrosse.
Women's basketball
Limestone's women's basketball program has made 5 consecutive appearances in the NCAA Division II National Tournament, reaching the elite eight in 2014, and the final four in 2015.
Football
On October 26, 2012, Limestone announced they would add football and begin play in 2014. Bobby James, previously the defensive coordinator at Wingate University was named the inaugural head coach on December 14, 2012. After a "redshirt" season with players but only scrimmages, Limestone began NCAA Division II play in the fall of 2014 and recorded a record of 2–9, followed by a 2–8 season in 2015. James left the program in early 2016, and on May 11, 2016, Limestone College announced the hiring of former National Football League wide receiver Mike Furrey as the second head coach for the Saints. Furrey was previously wide receivers coach at Marshall University and a former head coach at Kentucky Christian University. Under Furrey, the Saints went 5–6 in his first season, followed by a 4–6 campaign in 2017. He departed the team in January 2018 to become the wide receivers coach for the Chicago Bears. The Saints compete in football as an independent, but during the 2015–2018 seasons have arranged a scheduling agreement with the South Atlantic Conference to provide most of their contests. In April 2017 the Limestone Saints were announced as the first associate member of the South Atlantic Conference, and began competition in the SAC beginning in fall 2017.