This study is qualitative in nature and has applied questionnaires, interviews methods and literature reviews to gain information. Thus, twenty four (24) participants were purposefully sampled to participate in the study about challenges faced by QAUs in tertiary education. Generally, availability of resources (fund, personnel, information and physical), internal and external process, involvement of varied stakeholders and poor perception on QAU are challenges faced by QAUs in tertiary education. This implies that, quality of tertiary education cannot be reached due to unsorted challenges faced by QAUs leading to poor quality of graduates and mismatch with skills and knowledge required in the labour market. Therefore, institution’s management plays a great role in developing quality culture and supporting QAU in enhancing quality results in achieving mission, vision and goals