The paper investigates the impact of the cost allocation method on the economic results of CHPs operating in Russian energy markets. The distribution of costs between the electric and heat energy were calculated for each of the CHP’s operational modes by the exergy, physical and electrical equivalent methods. When CHP operating in winter physical and electrical equivalents allocation methods are equally effective. Using the exergy method of cost allocation for the given initial data led to the CHP falling behind the trading schedule of the wholesale power market and to a significant reduction in the income from production and business. When the CHP operates during the transition period, it incurs losses from production and business. Even though using the physical method allows the CHP to catch up with the trading schedule of the wholesale power market, the profit from the electricity sales is not high enough and does not cover the substantial losses incurred by the power plant in the local heat market. At the same time, using the exergy method and the method of electrical equivalents lets the CHP profit in the heat market, significantly reducing losses resulting from the non-payment of electricity on the wholesale power market. When the CHP operates in the summer period it incurs serious losses of production and economic activity. In this case, using cost allocation methods leads to the same economic results. Despite the fact that using the exergy method allows the CHP to make a profit from selling thermal energy in the heat local market, the heavy losses from non-payment of electricity on the wholesale power market do not allow to benefit from this cost allocation method compared to other methods. In general, the method of electrical equivalents provides the greatest economic benefit during the year, allowing to form a compromise solution for the allocation of costs between heat and electricity.