The modern economy is characterized by variability, uncertainty, and instability. Accordingly, companies need highly qualified personnel who are able to work in a new environment and participate in a continuous process of change. This aspect concerns managers who set the vector of the company’s development, and their every decision in response to changes in the internal or external environment determines the future of the company, its economic and strategic indicators. In response to these requirements, modern universities need more and more tools to influence the formation of the necessary competencies among students, but the speed of transformation of educational programs and the introduction of innovative approaches at universities is much lower than the conditions of the modern economy require. This study is a continuation of the author’s model of improving and transforming educational programs for training modern managers in a dynamic economy. The study develops and describes the structure of training managers at the master’s degree stage, and also forms and describes a model of inter-program training as a tool for obtaining practice in developing and implementing real projects and, accordingly, developing management skills.