The article describes the relevance of the introduction of internal audit at agricultural enterprises in order to successfully develop rural areas. The classification of principles is considered and the functions of the internal control system at agricultural enterprises are defined. The methodology of internal control aimed at improving the performance of agricultural enterprises is proposed. Because internal audit is entrusted with the function of ensuring the integrity of decisions made and their execution, based on information about the activities of the organization, the function of interconnection, informing about the implementation of management decisions. One of its components, food security, plays an important role in ensuring Russia's national security. Ensuring food independence is possible with the effective development of agricultural organizations, which involves both the production of high-quality food products and the implementation of existing in-house reserves. In the context of the increasing role of food security in Russia, the importance of the internal control and audit system in agricultural organizations is increasing. Market relations determine the objective need to increase the role of accounting in enterprise management. Timely, reliable and analytical information is needed to make operational and tactical decisions on enterprise management in conditions of constantly changing market conditions and developing competition among producers. With the development of market relations, accountants were "flooded" with a stream of regulatory documents regulating the legal issues of the activities of agricultural enterprises, the organization and setting of accounting for the latter, the formation of their reporting and taxation. In this regard, it became necessary to create an internal control service at the enterprises of the agro–industrial complex - a form of non-governmental control over the activities of enterprises. Internal audit is entrusted with the function of ensuring the integrity of decisions made and their execution, based on information about the activities of the organization, the function of interconnection, informing about the implementation of management decisions. The main importance of internal audit technology and methodology lies in the constant monitoring of management processes and their analysis. Thus, the problems of effective organization and improvement of the internal audit methodology contribute to increasing the effectiveness of information communication in the management system in order to coordinate economic processes in accordance with the chosen development strategy of an agricultural organization.