Reducing the level of import substitution is one of the important issues of the Russian agro-industrial complex development. In this regard, there is a need to find new management methods for regional agro-industrial systems with an emphasis on their interaction with retail chains and industrial enterprises. Creating comfortable conditions for the integration of economic entities in the regions is one of the aspects of management. These conditions include the retail networks development, the availability of legal mechanisms for organizing network systems and the development of the business investment environment. The article is devoted to the issues of enterprises network interaction in the agro-industrial complex, as one of the promising areas of development in a crisis economy, namely, assessing the effectiveness of associations.