Decentralization of Brazil's Unified National Health System (SUS) still poses challenges in large cities. To characterize decentralization as an essentially political process, institutional policy variables, including local management capacity, are determinant for shaping decentralization in each context. Using the government triangle reference to evaluate management capacity, a case study was conducted with the objective of analyzing the system's decentralization in the city of São Paulo, Brazil's largest metropolis. An analysis of selected health system managers and administrative documents identified a trend towards focusing health management at the municipal level in 2005-2008, accompanied by dismantling of local/regional structures in the Municipal Health Secretariat, resulting in technical and policy depletion at these levels. Despite the limits of decentralization, the article emphasizes its power as an operational strategy to achieve the SUS' objectives. The article also stresses the need to resume the health decentralization process in the city of São Paulo, both moving towards local/regional levels and linked to the decentralization of municipal public management.