The college began its first season in the NAIA as a four-year institution in 2018, joining the NAIA as an Independent within the Association of Independent Institutions (AII) from 2018–19 to 2019–20. Prior joining the NAIA, the Lynx were a member of the National Junior College Athletic Association (NJCAA) and its primary home conference was the Mid-West Athletic Conference (MWAC), stemming from its many years as a junior college. Prior to that, Lincoln College was a member of the Illinois Intercollegiate Athletic Conference (IIAC) from 1910–11 to 1927–28.
