- Agribusiness Management Department
- Agricultural Education and Extension Department
- Agricultural Engineering Department
- Animal Science Department
- Plant Science Department
- Accountancy Department
- Economics Department
- Management Department
- Marketing Department
- Elementary Education Department
- Home Economics Department
- Integrated Laboratory School
- Secondary Education Department
- Chemical Engineering Department
- Civil Engineering Department
- Electrical Engineering Department
- Mechanical Engineering Department
- Fisheries Department
- Fisheries Technology
- Environmental Science Department
- Forestry Department
- Forestry Technology Department
- Midwifery Department (Defunct)
- Nursing Department
- Hotel Restaurant Management Department
- Computer Studies Department
- Information Systems Department
- Internet Services Center
- Support Services & Training Department
- Biology Department
- Chemistry Department
- Mathematics Department
- Physics Department
- Community Development Department
- Public Administration Department
- Social Work Department
- Communication & Media Studies Department
- English Department
- Filipino Department
- History Department
- Library & Information Science Department
- Philosophy Department
- Political Science Department
- Psychology Department
- Sociology Department
- Physical Education Department
- Graduate (CBA)
- Graduate (CED)
- Graduate (CHS)
- Graduate (CNSM)
- Graduate (COA)
- Graduate (CPA)
- Graduate (CSPEAR)
- Graduate (CSSH)
- Graduate (ISED)
- Graduate (KFCIAAS)
- International Relations Department
- Islamic Studies Department
- Teaching Arabic Department
- MSU – Institute of Science Education
- MSU ISED – Regional Science Teaching Center
- MSU ISED – Science High School
DIVISION OF ENGINEERING TECHNOLOGY (Under the Supervision of College of Engineering)
- Metal Department
- Wood Department
HIGH SCHOOL (Secondary)
- MSU-Balindong Community High School
- MSU-Baloi Community High School
- MSU-Binidayan Community High School
- MSU-Malabang Community High School
- MSU-Marantao Community High School
- MSU-Masiu Community High School
- MSU-Saguiran Community High School
- MSU-Siawadatu Community High School
- MSU-Tamparan Community High School
- MSU-Taraka Community High School
- MSU-Tugaya Community High School
- MSU-Wao Community High School
- MSU-Integrated Laboratory School (Secondary)
- MSU-ISED Science High School
- MSU-University Training Center (Secondary)
ELEMENTARY SCHOOL
- MSU-Integrated Laboratory School (Elementary)
- MSU-University Training Center (Elementary)
