The article reports the results of a comprehensive RFBR project which combined research in the fields of soil science, forestry, botany, ecology, microbiology, and economics. The question of monetization of ecosystem services and the challenges that occur when interpreting the results based on the integration of natural sciences and economic approaches in the study of this problem are investigated. This discussion highlights the need for a better statistical tool to shift the focus in measuring economic phenomena to sustainable development. We propose a system of mappings based on model (operational) relationships between functional and structural features of the soil and external data, each of which is characterized by a certain set of interacting processes. The theoretical and empirical background for studying changes in the land-use regime and the carbon balance in ecosystems is explored. Changes in the morphological, basic agrochemical and microbiological properties of soils, as well as the reserves of organic carbon and microbial carbon in the top-meter layer of soil in various land-use scenarios are shown. The total carbon budget was estimated for sites with different land uses on genetically similar soils in the middle-taiga subzone of European Russia. Indicators of the state of the soil system, which can be used for the economic assessment of landuse change are proposed.