[3][4][5] Bethesda University is a member of the National Christian College Athletic Association (NCCAA).

Their men's basketball team was a member of the now defunct Pacific Christian Athletic Conference (PCAC).

Both women's basketball and baseball have reached the NCCAA's national tournament championship game in 2015 and 2016.

In 2016 and 2021, BU men's basketball, led by Filipino coach Leo Balayon, became only the second non-NCAA/NAIA program in history to upset an NCAA Division 1 program twice when it defeated Cal State Northridge of the Big West Conference on two occasions.

[11][12] Balayon is the first individual, born and raised in the Philippines, to become a head men's basketball coach in the United States.