The article presents an analysis of the development problems of project-based learning technology in Russian universities, which can make a significant contribution to achieving the goal of academic leadership. The issues of the formation of the competencies of a university graduate in the context of project-based learning are considered. It is shown that project-based learning should be included in a multifactor educational environment - the innovative ecosystem of the university. The relationship between the elements of the university’s innovation ecosystem, such as education, individual learning path, project-based learning, digital content, polylingual content, non-formal education, partnership programs, supervising, mentoring, design and interdisciplinarity, has been determined. The article substantiates the criteria for the effectiveness of project-based learning, and also offers options for the formation of the innovative ecosystem of the university, as a new trend in the Russian educational environment, which allows students to be involved in research and project work.