The article is devoted to the development of a comprehensive methodology for assessing and auditing a company's logistics costs, in the context of economic uncertainty and geopolitical changes, based on the integration of the Total Cost of Ownership (TCO) principle and the Balanced Scorecard (BSC). Logistics audit is described as a process of identifying bottlenecks, relationships between functional elements of the logistics system and GAP analyses. Special emphasis is placed on audits of procurement, transport and warehouse logistics. Attention is paid to the formation of an integral qualitative indicator of logistics services, which is normalized on an immeasurable scale and compares different performance parameters. The proposed approach overcomes the fragmentation of traditional cost accounting and provides a balanced assessment of the logistics system's performance against financial and operational criteria. As a result, it forms a scientifically grounded basis for managerial decision-making aimed at minimizing total logistics costs while achieving the target service level.