The contribution presents selected outputs of the scientific research activities of its authors in the field of implementation, intensification, and standardization of environmental management systems for technological enterprise practice. Aspects of environmental-economic continuity were examined in assessing technological inputs in the form of cost accounting for material and energy flows and the level of environmental quality of transformation processes in the input-output enterprise system. Based on this, a model for accounting for the costs and revenues of individual processes was proposed and standardized. The methodological approach to cost accounting consists of ten key elements arranged in Deming's cycle of continuous improvement with a closer specification of their purpose, function, and content. The basis for modelling and quantifying material and energy flows is the determination of input/output points, processes, and the determination of quantification nodes for evaluation in physical and monetary units. For each quantity node, costs for the system and waste management must also be quantified. Energy costs, system costs, and waste management costs are divided into product and material losses from production cost data for each quantity node. Summarization and integrated presentation of cost data are proposed to utilize cost matrices and Sankey diagrams. Further benefits of using environmental cost accounting for material-energy flows in production are also specified.