JRMSU consistently endeavors for quality assurance. Accreditation of several programs by the Accreditation Agency of Chartered Colleges and Universities in the Philippines (AACCUP), and International Organization for Standardization (ISO) is made possible. Technical-Vocational courses are also accredited by the Technical Education and Skills Development Authority (TESDA).
| Programs | Accreditation Status | Accrediting Agency |
| Dapitan Campus | ||
| Bachelor of Science in Marine Transportation | Certified ISO 9001:2008 | Global Group |
| Bachelor of Science in Marine Engineering | Certified ISO 9001:2008 | Global Group |
| Bachelor of Elementary Education | Level I | AACCUP |
| Bachelor of Science in Secondary Education | Level II | AACCUP |
| Bachelor of Science in Criminology | Level I | AACCUP |
| Bachelor of Science in Hotel & Restaurant Management | Level I | AACCUP |
| Dipolog Campus | ||
| Bachelor of Science in Criminology | Level I | AACCUP |
| Bachelor of Elementary Education | Level I | AACCUP |
| Bachelor of Science in Hotel and Restaurant Management | Level I | AACCUP |
| Bachelor of Science in Industrial Technology | Candidate Status | AACCUP |
| Katipunan Campus | ||
| Agricultural Technology | Level II (Re-accredited) | AACCUP |
| Secondary Education | Level II (Re-accredited) | AACCUP |
| Tampilisan Campus | ||
| Bachelor of Elementary Education | Level I | AACCUP |
| Bachelor of Secondary Education | Level I | AACCUP |
| Bachelor of Science in Agriculture | Level I | AACCUP |
| Siocon Campus | ||
| Bachelor of Science in Criminology | Level I | AACCUP |
| Bachelor of Science in Computer Science | Level I | AACCUP |
| Bachelor of Science in Secondary Education | Level I | AACCUP |
| Bachelor of Science in Elementary Education | Level I | AACCUP |
| Bachelor of Science in Industrial Technology | Level I | AACCUP |
| Bachelor of Science in Agriculture | Candidate Status | AACCUP |
| Bachelor of Science in Hotel & Restaurant Management | Level I | AACCUP |
ISO Accreditation/ TESDA Registered Programs
To satisfy its customer in Maritime Education, the University embarked on ISO accreditation which was successfully granted with certification on June 4, 2009 and valid until May 4, 2012 by the Anglo Japanese American Registrars based in England. The ISO Certification is an evidence of the implementation of quality management system for Maritime Education in the university. On the other hand, JRMSU-Siocon Campus has eleven (11) TESDA registered programs namely: Health Care Servicing NC II, Computer Hardware Servicing NC II, Household Servicing NC II, Housekeeping NC II, Building Wiring Installation NC II, Automotive Servicing NC II, Shielded Machine Arc Welding NC II, Machining NC II, Food and Beverage Servicing NC II, and Garments Construction. The Main Campus has five (5) TESDA registered programs namely: Driving, Caregiving (Health Care Service NC II), Garments Construction, Food Preservation and Welding.