Embedding quality into higher education institutions is a challenging matter given the complexity of the higher education environment. Although several studies have been conducted seeking to reveal associated challenges, a limited number of researches have been implemented on a cross-national level. This study investigates challenges associated with implementing quality in European higher education institutions as well as exploring the differences amongst them. The methodology involved qualitative analysis for 40 expert interviews coupled with employing 'triangulation of source' procedure to assure the reliability of the findings. Furthermore, the results are quantified to investigate the frequency of challenges. These challenges are discussed under three broad categories: (1) organisation challenges that include quality system, educational system and external stakeholders; (2) implementation challenges including execution, competency and funding challenges; (3) leadership and quality culture challenges. The article relates the challenges to quality in European higher education and the ways to overcome them.