This research aimed to investigate the relationship between students’ perceptions of the quality of different aspects of higher education institutions, satisfaction of their psychological needs, and satisfaction with their studies at the higher education institution in question. This research involved 404 students of humanities, social sciences, and interdisciplinary studies. A Croatian version of the HedPERF Scale was used to examine the perceived level of quality of the higher education institution and the Basic Psychological Needs in the Academic Context Scale to check if students’ basic psychological needs were satisfied in the academic context. The obtained results suggest that satisfying students’ psychological needs at higher education institutions is important for their overall satisfaction with their academic studies but also that this relationship is mediated by the perceived quality of different aspects of the higher education institution in question, at least when it comes to the needs for autonomy and relatedness. A positive connection was also confirmed between satisfaction of students’ psychological needs and perceived level of quality, and the perceived level of quality of and satisfaction with academic studies. The research results confirm the importance of investing in the quality of higher education institutions, in different aspects, to improve students’ well-being and satisfaction with their academic experience, which in turn will positively affect their academic outcomes.