This article is devoted to the selection and justification of priority applied control tasks in the automation of a biogas plant (BP), taking into account the risks of loss of control. The types of technological risks in the management of fermentation processes in methane tanks are considered. A reasoned analysis of quantitative risk assessments using the pairwise comparisons method is carried out. The use of the method of consistency of expert opinions in the algorithm for solving the problem of selection and justification made it possible to conduct a strict analysis of the consistency of expert opinions and to identify whether the obtained estimates are random or not. Using the obtained information models for the regime parameters of anaerobic digestion processes, the relevance of developing a better control system for the optimal temperature regime of substrate heating, temperature stabilization in the methane tank, and the rational end time of the fermentation process is justified. The results obtained are in the best agreement with the improvement of the BP process management efficiency.