NNU has a long and distinguished history as an accredited institution. Having first been accredited by the Northwest Commission on Colleges and Universities (NWCCU), a regional accrediting body recognized by the Council for Higher Education Accreditation (CHEA). NNU was accredited as a junior college in 1930, and subsequently as a four-year college in 1937. NNU has maintained its regional accreditation with the NWCCU since that time.
In addition to regional accreditation, the following departments are accredited by nationally recognized specialized accrediting boards:
- Business - NNU's undergraduate and graduate business programs are internationally accredited by the Accreditation Council for Business Schools and Programs (ACBSP), with the exception of the Associate of Arts in Accounting and the Associate of Arts in Business.
- Counseling - NNU's counseling program areas are nationally accredited by the Council for Accreditation of Counseling and Related Educational Programs (CACREP). The school counseling program is approved by the Idaho State Board of Education to provide for institutional recommendation for state certification in Pupil Personnel: Counseling. Upon graduation, students in the Clinical; School; and Marriage, Couple, and Family program areas have all the coursework necessary to apply for Licensed Professional Counselor (LPC) in the state of Idaho. Marriage, Couple, and Family Program graduates may also apply for the AMFT certification in the State of Idaho. The post-graduate pre-certification program in Play Therapy prepares students for APT certification at the national level.
- Education - NNU is nationally accredited at the bachelor's degree level and higher by the Council for the Accreditation of Educator Preparation (CAEP). Additionally, the education programs are approved by the Idaho State Board of Education to provide for institutional recommendation for state certification in Elementary Education, Secondary Education, Special Education, and School Administrator (Pre-K-12 Building Principal, Director of Special Education, and Superintendent).
- Engineering - NNU's undergraduate engineering program is nationally accredited by the Accreditation Board for Engineering Technology (ABET).
- Northwest Nazarene Divinity School - Northwest Nazarene Divinity School has the historic distinction of being the first institution with fully online programs ever to be granted full membership by the Association of Theological Schools (ATS).
- Nursing - NNU's undergraduate and graduate nursing programs are nationally accredited by the Commission on Collegiate Nursing Education (CCNE).
- Social Work - NNU's undergraduate and graduate social work programs are nationally accredited by the Council on Social Work Education (CSWE).