The problem of operational planning of a biogas combined heat and power (CHP) plant under conditions of limited biofuel resources is analyzed in this paper. The power plant operation mode depends on the biomass amount and its delivery. Consideration of parameters with high dispersion, such as the ambient temperature, thermal energy consumption and energy price, makes the problem solution much more complicated and requires new algorithms and software tools. This paper proposes an algorithm of stochastic optimization to estimate the maximum value of income by taking into account the random nature of variables. When the biomass resource is limited, the need of its optimal distribution for all the time periods considered becomes of top importance. In this paper, a case study is conducted on a realistic biogas CHP plant that demonstrates the feasibility of our stochastic optimization algorithm. It is concluded that the proposed algorithm can increase the efficiency of the biogas power plant operations under conditions of limited resources. The main distinction of this paper is that a biogas CHP plant optimization model is considered from the point of view of income maximization under market conditions taking into account the limited biomass resources.