The development of digitalization and the widespread intense implementation of digital ecosystems are an integral part of the successful economic development of enterprises and regions of the country as a whole. However, it should be noted that for the majority of the workforce, this process is accompanied by certain costs and difficulties. Modern technologies, such as artificial intelligence, robotics, and automation of processes, not only increase efficiency and productivity but also require new skills and competencies from the employees of enterprises.In the context of digitalization, universities are faced with the task of training cross-functional specialists with knowledge in informatics, mathematics, and economics, who can meet the challenges of digital transformation of business and production. To solve such problems it is necessary to use not only new pedagogical technologies but also new training programs for future specialists. The program “Intelligent management systems for enterprise digital ecosystem” presented in the article for master’s degree training in 09.04.03 “Applied Informatics” is aimed at practice-oriented training in the conditions of Industry 4.0 and developing students’ interdisciplinary competencies in the field of IT solutions management, systems engineering, and economics. The program was developed taking into account labor market needs and active cooperation with manufacturing enterprises, which is reflected in its structure. In particular, the main part of the educational process under the program is focused on practice: project preparation and research work.