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Using the example of developed “Biotechnical systems and technologies” master educational program the ability to develop the students’ innovative activity through the implementation in the of practice interdisciplinary commercial projects using the production base of modern innovation and implementation centers of the Federal University is demonstrated. Such an organization of educational activities marked a pronounced practice-oriented orientation of education, allowed the undergraduates to develop certain entrepreneurial skills, improved the perception of educational material. Based on specially developed criteria the analysis is carried out and assessment of training effectiveness is taken according to such parameters as educational program productivity and relevance as well as the graduates’ satisfaction with acquired knowledge and skills. It is demonstrated that the project activity technology forms important professional experience for the masters and contributes to strength the social partnership with specialized organizations.