In the context of a dynamically developing competitive market, global changes in production and the distribution of production resources, the increasing influence of political and socio-economic factors, the issues of ensuring the economic security of both the region and the industries included in its economy acquire special relevance. Agriculture is, on the one hand, the most vulnerable sector of the economy and is influenced by many factors, but, on the other hand, the most significant for the sustainable development of the Altai Territory. The study concluded that it is highly competitive and dependent in food security in other regions of the Siberian Federal District and the dynamics of development of the agro-industrial complex of the region. However, there are threats to economic security, the presence of which impedes the effective functioning of the agro-industrial complex. Based on the study, the main risks and threats have been identified that are of the greatest importance for the economic security of agriculture in the Altai Territory: a low level of investment activity, deterioration of agricultural machinery, a shortage of qualified personnel, risks of natural factors.