The article deals with the issues of the practical application of industrial information system, namely, Enterprise Resource Planning (ERP) in the management of the economy of a diversified agro-industrial complex in the risk farming area. Features of ERP system application are considered taking into account both multidirectional activity of the agricultural enterprise (crop production, animal husbandry, and industrial production), and the complex system of taxation: the presence of a common taxation system and taxation of various activities. Particular attention is paid to the mechanism of closing accounts, and the formation of the actual cost in terms of agricultural production, which is not so much complicated as a laborious and routine task. A huge number of transactions, multiple calculations of the costs distribution bases, the complex structure of the divisions of the very enterprise make the task of automating of process closing period extremely important. The article presents the experience of both the use of ERP system and the training method of specialists in the use of such industrial information systems for automated accounting and management accounting, payroll and personnel accounting, tested at St. Petersburg State University. In consequence of the implementation of the algorithms described in the article, one managed to achieve an increase in both quantitative economic indicators of the agricultural complex, and qualitative indicators, related to the training of specialists in the field of application of ERP systems in agro-industrial complexes.