One problem about developing circular economy in the mineral resources sector is the absence of a methodological approach to forming an organisational economic mechanism for circular subsoil use in Russia and its regions which specialise in the extraction of minerals. The paper aims to create such an approach. The concept of circular economy and theoretical propositions of natural resources economics and environmental management constitute the methodological basis of the research. The methods include analysis, synthesis, and inductive reasoning. The paper justifies the application of the terms “organisational economic mechanism”, “circular subsoil use”, and “organisational economic mechanism of circular subsoil use” and provides them with definitions. Then, the article identifies organisational, legal and economic factors affecting the organisational economic mechanism, as well as formulates principles of balancing it and ensuring its efficiency. Proceeding from these factors and principles the authors justify their selection of tools: 1) organisational and managerial ones targeted at forming, regulating, and coordinating the activities of circular processes’ participants; 2) economic ones that create material incentives for developing circular economy in the subsoil use. According to the research results, there are two groups of indicators showing the effectiveness of using these tools: general economic (macroand meso-) and commercial (microeconomic) indicators. The developed methodology allows ensuring the effectiveness and efficiency of the state management of secondary resources and waste generated by mineral extraction.