The merging of the China Province Jesuits in the Philippines and the Philippine Province Jesuits in 1988 facilitated the assignment of Filipino Jesuits to the three Chinese-Filipino schools: Xavier School (San Juan, Metro Manila), Sacred Heart School–Ateneo de Cebu and the Santa Maria Catholic School (Iloilo). In June 1991, Fr. Renato Puentevella, S.J. succeeded Fr. Chi as Director - Principal. During his five-year term, SMCS went through the Philippine Accrediting Association of Schools, Colleges and Universities (PAASCU) Preliminary Survey and Formal Survey. The Grade School Department was granted a three-year PAASCU accreditation in 1995 and the High School Department followed suit the following year. Fr. Enrique Ma. Lalana, S.J. was appointed Director-Principal and Fr. Manuel A. Uy Jr., S.J. school chaplain and parish priest in June 1996. In November 1999, SMCS applied for PAASCU re-accreditation and was granted five years.
In the year 2000, Fr. Manuel A. Uy Jr., S.J. assumed the post of Director-Principal. Fr. Robert Exequiel Rivera, S.J. became the school's chaplain for a year. When Fr. Emerito Salustiano de la Rama, S.J. came in 2001, he was appointed Assistant Director and the following year assumed the position of Principal of the Grade School Department. For the school year 2004-05, Mrs. Aurora de la Cruz was appointed Principal of the high school department. In November 2004, PAASCU conducted a resurvey visit. Both the Grade School and the High School Departments have been granted re-accreditation for 2005-2010.
On April 30, 2004, a Memorandum of Agreement was signed by Jesuit Father Provincial Romeo J. Intengan, Fr. Manuel A. Uy Jr., S.J. Director of SMCS, and Mr. Victor F. Pison of the Kauturan Pison Development Corporation (KAPIDECO). Archbishop Angel N. Lagdameo of the Archdiocese of Jaro and Iloilo City Mayor Jerry Treñas, an Ateneo de Manila alumnus, witnessed the MOA signing which formalized the establishment of an Ateneo de Iloilo - Santa Maria Catholic School in its new location in Mandurriao, Iloilo City.
In School Year 2009-2010, Fr. Emerito Salustiano de la Rama, S.J. succeeded Fr. Manuel A. Uy, S.J. as the new school president. Fr. Uy was elected by the Board of Trustees of Sacred Heart School - Ateneo de Cebu to become their school director.
This School Year 2012-2013, Fr. Joseph Y. Haw, S.J., takes over the school presidency.
A new school site is being built on a 7.5-hectare campus in Brgy. San Rafael, Mandurriao, Iloilo City. The place (Phase 1) is now being used by the High School Department. Construction of the Grade School and Administration buildings (Phase 2) is to start anytime in 2013.
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