This article analyzes the organizational and methodological mechanisms aimed at increasing the effectiveness of the activities of departments of higher educational institutions in the context of transformation. Such aspects as the digitalization of the educational process, the development of research activities, the improvement of the qualifications of professors and teachers, and the introduction of an effective management system will be studied. According to the research results, these approaches serve as an important factor in improving the quality of higher education. Also, the opinions of local, CIS, and foreign scientists were analyzed, and best practices were studied.