From classes held in an old building and a portion of a convent, the school built modern structures while retaining classic features.

Established by the Order of Augustinian Recollects in Cebu City in 1947, the then Colegio de San Jose - Recoletos held classes in a portion of a convent, which can be traced back on 1621, and in an old building.

The Augustinian Recollects decided to construct a new college building designed by architects Imelda Borromeo and Mariano Monasque.

In 1980, CSJ-R bought a new site in Basak Pardo, Cebu City, then built the new building for the grade and high schools, the Recoletos Coliseum, Open Gymnasium and the Pope Paul II Retreat House.

Roughly three years later, the Recoletos Coliseum (now fully air-conditioned) was completed, making June 1984 a significant date for sports enthusiasts.

The university's College of Nursing held its 1st Capping, Badge Investiture and Candle Lighting Ceremony in June 2006 at the Recoletos Coliseum, Basak Campus.

On November 28, 1998, the 52nd General Chapter held in Granada, Spain, voted for the creation of a new Religious Province in the Philippines dedicated to St. Ezekiel Moreno, OAR.

In 2022, the University of San Jose–Recoletos secured a prestigious victory at the Philippine Startup Challenge 7, hosted by the Department of Information and Communications Technology.

They developed an innovative mobile application named 91Watch, an emergency hailing platform that uniquely incorporates mesh networking technology.