By 1991-92, the university, under the leadership of the new president, Dr. Ronald R. Duterte, decided to reopen college operations phasing in the courses by year levels; that is, first year of all recognized courses was offered during this school year; first and second year by 1992-93, and so on until all years are opened.
In 1990 transfer of the college to Lahug Campus was completed; in 1993, the Computer Studies Center was inaugurated. In 1994, Bachelor of Science in Computer Science was offered; in August 1996, the USP Alumni Hall which houses the famous Rizaliana Museum was inaugurated. February 1995, USPF opened the non-academic skills-based Continuing Education Department, now the Learning Resource Center in partnership with the Manpower Resource Center, now TESDA; in June 1999, the College of Law reopened and a new graduate program, Master of Science in Environmental Management was offered.
In 2002, the ground breaking was done for the new building that would house the College of Nursing, College of Computer Studies, College of Law, College of Engineering, and the Theater for Performing Arts.
In 2003, the College of Nursing started in its initial operation and its doing well. On March 5, 2004, the Commission on Higher Education (CHED) issued a permit for USPF to open and conduct first and second years of the four-year Bachelor of Science in Pharmacy starting June 2004, on March 19, 2004, CHED issued a permit for USPF to open and conduct Diploma in Professional Education (DPEd) and Diploma in Special Education (DSPEd). On June 10, 2005 CHED issued Government Recognition for USPF to conduct and operate the post baccalaureate diploma in Community Development effective academic year 2005-2006, on the same date, CHED also issued a permit to open and conduct first year of the four-year course in Bachelor of Science in Entrepreneurship effective Academic Year 2005-2006. On November 20, 2005, the university president Dr. Ronald R. Duterte died, on December 1, 2005 the Board of Trustees appointed Dr. Alicia P. Cabatingan as the new president. In 2006, the College of Arts and Sciences and the College of Education successfully passed the PACUCOA Level I Accreditation during a visit February 20–22, 2006.
In school year 2007-2008 University of Southern Philippines triumphed over the nationwide results of two of the most prestigious Licensure Exams, the same year the university processed the accreditation of five departments: School of Business and Management, College of Computer Studies and Information Technology and the Basic Education of Mabini and Lahug campuses. In 2009, USPF started Bachelor of Science in Hotel and Restaurant Management, Bachelor of Science in Nutrition and Dietetics, and Bachelor of Science in Computer Engineering. The College of Computer Studies and School of Business and Management was granted Level I Status by the Philippines Association of Colleges and Universities Commission on Accreditation in 2014. In school year 2010-2011, two programs were granted Level II Accreditation Status: the Bachelor of Secondary Education and Liberal Arts Programs and Level I Status for the Bachelor of Elementary Education, after the Level II Formal Visit of the Bachelor of Secondary Education, PACUCOA accelerated the program for LEVEL III Format Visit on February next year April 2016.
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