The integration of the Kyrgyz Republic into the Eurasian Economic Union (EAEU) will permit the country to most optimally combine the diversity of natural, economic, intellectual, and other resources into a single system. However, within the framework of the EAEU, the food security of the country depends mostly on ensuring the conditions for effective functioning of the agro-industrial complex, effective implementation of its potential to optimize the volume of production of competitive agricultural products and food necessary to meet the needs of the population and processing industry, and reduction of dependence on food imports. This study aims to identify the key food security issues of the Kyrgyz Republic in the process of its integration into the EAEU. To this end, the study identifies key changes in the agro-industrial complex and reveals the interests of potential stakeholders (the political elite, business, actors in the agricultural production sector, population, etc.) in strengthening food security. To improve food security of the Kyrgyz Republic in the process of its integration into the EAEU incorporating the best interests of all stakeholders, the following policy options were offered: (i) to create a system of procurement depot complexes; (ii) to expand the transportation systems and replace the vehicle fleet; (iii) to reform veterinary and phytosanitary systems; (iv) to support the food security atlas; (v) to actively participate in the Scaling Up Nutrition (SUN) Movement; and (vi) to strengthen the social protection system to reduce poverty in rural areas. The food security situation in the country was forecasted based on current trends and factors as well as proposed recommendations, which were prepared during this case study. In making decisions, the Government of the Kyrgyz Republic must take into account the interests of all stakeholders in an optimal manner and, at the same time, must understand that integration into the EAEU does not deprive political elites of their independence in making management decisions. All proposed policy options will help develop the agro-industrial complex of the country and strengthen its food security; however, it is expected that the most productive options include creating a system of procurement depot complexes; reforming the veterinary and phytosanitary systems; developing the transportation system; and strengthening the social protection system to reduce property in rural areas. Implementation of these policy options will help agricultural producers of the country enter the common agricultural market as well as help the government improve quality of the agricultural output, reduce dependence on imports, increase exports, reduce social tensions, and supply quality food products to the population of the country.