The article considers approaches to the development of criteria for assessing the quality of scientific research in St. Petersburg Mining University, Russia (Mining University), the functioning of which contains the main features of research university as well as of a scientific organization. The research methods include expert assessments, analysis and synthesis and other desk research methods. Based on the analysis of the results of the scientific activity of the organization in recent years, a set of basic quantitative indicators has been developed, as well as a set of additional qualitative indicators of the effectiveness of the scientific departments of the university. Qualitative indicators, including the rating assessment of the research carried out by the Scientific and Technical Council of the university, are designed to complement the widely used scientometric data. Thus, scientometric, financial indicators and a comprehensive (multifactorial) qualitative assessment can serve as criteria for the quality assessment for the scientific activity of the university. The information obtained is relevant for the formation of a quality management system for scientific research at Mining University, as well as for other research universities with a similar organizational structure. However, the conclusions obtained cannot be automatically extended to the procedures for the formation of quality management systems for scientific research in organizations of a different profile.