The newest directions for evaluating the ecological and economic behaviour of agricultural enterprises involve the full use of by products, such as biomass. The main items of biomass costing (for the example of baled corn) are identified: the cost of corn waste in the field, the cost of twine for forming bales, the cost of fuel and lubricants, wages and social contributions, the cost of operation and depreciation of agricultural machinery, and other production and logistics costs. Based on the study of the structure of production costs that form the cost of biomass, it was found that the main share is made up of labour costs. With the purpose of complex optimization of the operating costs of agricultural activities, the necessity of introducing an innovative biomass cost management system based on automated accounting and analysis with the use of global positioning technologies, aerial monitoring with the help of drones, and the Internet of Things has been proven. The use of technologies for collecting and processing accounting information on agricultural activities for the formation of information arrays on the planned volume of harvested crops, salaries of operating personnel, fuel and lubricants, equipment depreciation and the need for routine maintenance of agricultural machinery, as well as additional operating and transportation costs, has been proposed. An innovative analytical model has been developed to study the impact of agricultural conditions (harvest volume, average wage of a production worker, distance from fields to storage or processing facilities, level of logistics organization, quality of agricultural products, level of use of the latest agricultural technologies and agricultural machinery) on production costs, which is the basis for operational and predictive innovative management of biomass costs. The innovation of the model lies in the use of linguistic variables, i.e., factors that are not quantifiable but can be economically evaluated. For the practical implementation of an innovative biomass cost management system, the use of the information scheme, which includes all the information components, on the basis of which managers develop and offer the best management solutions to minimize the cost of biomass, has been proposed. The need to reflect accounting and analytical information on the cost of biomass in integrated reporting (sustainability reporting) to inform internal and external stakeholders about the formation and use of alternative energy sources determines the prospects for further research in this area.