The set of agricultural segments of all subjects of the Russian Federation forms the basis for ensuring the country’s food security. The long-term strategy of risk-based development of agro-industrial clusters in the regions of Russia is built taking into account external and internal challenges, threats, risks and conditions of uncertainty. The main condition for mutually beneficial cooperation in the field of agriculture for the cluster members is the complementarity of production, service and trading enterprises. The network of interconnected agricultural and related industry enterprises within the framework of cooperation is more stable and generally competitive, concentrated on a limited area for the production of the final product. It is characterized by a combination of different industries, types of production, forms of ownership, a certain level of integration, and a common goal setting. The process of clusterization in agriculture is slow, but at the same time new jobs are being created, the technological park is being modernized and updated, and rural areas are actively developing. The advantages of the cluster system for agriculture are the integration of diverse enterprises, a combination of agriculture and animal husbandry, and cooperation between large, medium and small businesses. Agro-industrial cluster companies are able to jointly solve the tasks of creating added value, reducing transaction costs, minimizing unprofitable and duplicative processes, digitalizing agricultural work, and interacting with internal and external investors.