The article considers the changes taking place in almost all countries of the world, associated with the transition to a digital economy. The focus is on the peculiarities of higher education as the most important factor determining the opportunities for the development of any economic system. Currently, Russia has to modernize higher education in accordance with the needs of the labor market and further integration of Russian education into the global economic and educational space. The article confirms that universities have to change the educational paradigm in the developing digital economy. We have proposed a change from the outdated traditional models of educational activities to new ones that can stand up to the challenges of our time. We have formulated the main principles of organization of the educational process, such as the introduction of the competence approach into the educational process, use of methods of project-based learning, digitalization and informatization of education, the implementation of individual educational trajectories. We have considered the principle of forming professional competences through the integration of education, science, business structures and enterprises of high-tech industry on the basis of communities of teachers, students, and scientists. The proposed method of electronic portfolio (web portfolio) as one of the innovative teaching methods based on the formation of an individual educational trajectory. Analysis of the structure and interaction of the portfolio of the university allows to improve the system of criteria and indicators for estimating the efficiency of educational and scientific activities of faculties and institutes of the university, to streamline the organization and management of the university. Measures based on the principles offered will allow to implement new forms of training, increase the motivation of participants in carrying out scientific research and the efficiency of university’s management. This will provide the possibility of forming an innovative environment of the university on a qualitatively new level, and building a system of university management in accordance with the university’s tasks and taking into account modern trends. There is a plan to develop a mechanism of managing the innovative potential of the university in the nearest future in order to conduct personnel training on a fundamentally new quality level, taking into account contemporary tendencies.