The paper assesses the potential of cooperation between Russia and the countries participating in the EAEU in the agri-food sector. It is revealed that the share of agricultural organizations and food industry enterprises participating in joint projects to carry out research and development is much lower than in other industries. The weak interest of Russian enterprises in innovation activity has been noted. At the same time, in the agri-food sector, certain changes have emerged in the area of intensification of innovation activity. To this end, the study assessed the potential for cooperation in innovation in the agri-food sector. The reasons for the low rate of the digital transformation of the agri-food sector and the factors involved in these processes have been analyzed. © 2020, World Scientific and Engineering Academy and Society. All rights reserved.