[3] In 1985, John MacArthur became the school president; the name was changed to The Master's College, hoping to appeal to a wider evangelical audience.

[19] WASC reported a lack of qualified leadership and "a climate of fear, intimidation, bullying, and uncertainty" among faculty and staff as reasons for the probation.

[26] Chancellor John MacArthur has spoken and written at length in university publications about the threat he perceives from the gay agenda, asserting that "biblical love excludes homosexuality because of its sinfulness.

"[27] The Master's University is ranked among the worst American schools for LGBT students by LGBTQ Nation[28] and Campus Pride.

The university is a member of the National Association of Intercollegiate Athletics (NAIA), primarily competing in the Golden State Athletic Conference (GSAC) for most of its sports since the 2001–2002 academic year;[30] while its men's & women's swimming & diving teams compete in the Pacific Collegiate Swim and Dive Conference (PCSC).

The Master's compete in 18 intercollegiate varsity sports: Men's sports include baseball, basketball, cross country, golf, soccer, swimming & diving, track & field (outdoor) and volleyball; while women's sports include basketball, beach volleyball, cross country, golf, soccer, swimming & diving, track & field (indoor and outdoor) and volleyball.