The Commission works closely with other international and regional accrediting bodies. Institutions accredited by these bodies are also recognized by CUE. These include:
- Ministry of Education
- Higher Education Loans Board
- Kenya Accountants & Secretaries National Examination Board (KASNEB)
- Kenya National Examination Council (KNEC)
- Teachers Service Commission (TSC)
- Kenya Institute of Education (KIE)
- Institute of Certified Public Secretaries of Kenya (ICPSK)
- College of Surgeons of East,Central and Southern Africa
- The Institute of Engineers of Kenya
- Kenya Institute of Co-operative Management Engineers Registration Board
- Engineers Registration Board
- Medical Practitioners and Dentist Board
- Kenya Medical Laboratory Tecknicians and Technologist
- Higher Education Accreditation Council, Tanzania
- National Council for Higher Education, Uganda
- Council for Higher Education, South Africa
- Australian Quality Assurance Agency
- Lembaga Akkreditasi Negara (LAN)/National Accreditation Board, Malaysia
- Quality Assuarance Agency for Higher Education United Kingdom
- Middle States Association of Colleges & Schools Commission (USA)
- New England Association of Schools and Colleges (USA)
- North Central & Northwest Association of Colleges and Schools (USA)
- Southern Association of Colleges and Schools (USA)
- Western Association of Schools and Colleges (USA)
- Council for Higher Education Accreditation (USA)
- Distance Education and Training Council (USA)
- International network for quality assuarance agencies higher education
- International association of universities
- Association of Africa University
- University of Nairobi - The Deputy Vice-Chancellor (Administratrion and Finance)