The quality of the Master thesis developed by the students of the Entrepreneurship and Management to a large extent indicates the quality of knowledge, the level of skills and abilities of the graduates. In the article we consider our experience in supervising students' participation in the research projects and development of Master theses. Our analysis shows that participation in the scientific projects, parts of which become key research presented in the Master thesis, can substantially improve knowledge and research skills and abilities of the students, increase the quality of research and Master thesis per se and provides tangible benefits to the university and to the supervisor. Present research provides the analysis of the benefits gained as a result of graduates’ participation in the scientific projects as well as the analysis of the problems faced by the supervisor and the student such as insufficient level of knowledge and skills of the graduates or the necessity to reconcile the research topic with the study program. We also focus on the tasks, which most likely can be delegated to the students when involving them in the applied scientific projects. The results assure that the potential benefits received by the parties involved outweigh the headwinds faced by professors and the students when participating in the applied scientific research.