Today, the Manuel S. Enverga University is in the elite list of Autonomous Higher Education Institutions in the Philippines. The Liberal Arts-Commerce-Education programs have Level IV-accreditation status, the first and only in the Philippines accredited by the Philippine Association of Colleges and Universities Commission on Accreditation (PACUCOA).

The Civil Engineering, Industrial Engineering, Accountancy, Criminology and Law Enforcement, Computer Studies and the Institute of Graduate Studies and Research programs are Level 2-accredited.

The Bachelor of Science in Accountancy (BSA) program is Accredited Level II and all Commerce baccalaureate programs are Re-Accredited Level III. The College of Education is also PACUCOA Accredited Level III.

The basic education department is Level 1 accredited. In the pipeline is the accreditation to Level 1 of the College of Tourism and Hotel and Restaurant Management

The University is also a Center of Development (COD) in Information Technology, Teacher Education and Criminology programs.