Anaerobic fermentation in biogas plants is an effective and promising method of manure disposal. During fermentation, especially in the thermophilic mode, animal excrement is largely disinfected, pathogenic microflora dies, weed seeds lose their germination and, in addition, biogas is released, the utilization of which allows to obtain additional energy. This way of utilization of manure under the conditions of gradual depletion and increase in the price of traditional sources acquires special importance. Since fermentation is carried out in closed facilities, completely isolated from the surrounding environment, the possibility of the spread of infections and gases with an unpleasant smell and the ingress of untreated manure into the soil, ground and underground water is eliminated. As a result of the decomposition of organic substances in the fermented product, the share of biogenic elements increases, most of them turn into mineral substances easily absorbed by plants, and nitrogen losses do not exceed 3-5%. An experimental installation was developed to determine the nature of gas release, the depth of mineralization of organic matter depending on the regime and design parameters, as well as with the purpose of developing, based on the obtained dependencies, technological schemes for anaerobic treatment and waste disposal of animal husbandry enterprises. The theoretical basis of mathematical modeling and forecasting of the operation of bioenergy plants is the material balance equation related to the rates of biochemical reactions and flow rates. The derivation of the material balance equation is possible if there is information about the hydraulic characteristics of bioenergy reactors, which depend on the operating conditions, limitations, and final results of the process. In addition, data on the rate of flow of biochemical reactions, the influence of environmental conditions and operating parameters on them are also necessary.