The article assesses the potential for deepening the integration of the Eurasian Economic Union (EEU) member countries using the example of the agro-industrial complex, identifies integration and disintegration trends, as well as problems that impede the strengthening of partnership relations. The authors have analyzed state support measures aimed at solving these problems. The present study shows possibilities and directions of deepening integration based on the Russia's export-oriented import substitution policy. It was concluded that the development and improvement of measures of state support for the food industry and the agro-industrial complex should be formed considering the assessment of such supportive policy from the perspective of trade in value added. The authors have analyzed possible use of integration tools for enterprises of the agro-industrial complex. The study identifies industries with stable export potential. The analysis of the EEU export-import flows by disaggregated product segments shows the availability of mutual exchange of finished products within the same commodity group, which can be considered horizontal cooperation, but not vertical cooperation. © 2018, World Scientific and Engineering Academy and Society. All rights reserved.