There is little scientific evidence that urban upgrading helps improve health or reduce inequities. This article presents the design for the BH-Viva Project, a “quasi-experimental”, multiphase, mixed-methods study with quantitative and qualitative components, proposing an analytical model for monitoring the effects that interventions in the urban environment can have on residents’ health in slums in Belo Horizonte, Minas Gerais State, Brazil. A preliminary analysis revealed intra-urban differences in age-specific mortality when comparing areas with and without interventions; the mortality rate from 2002 to 2012 was stable in the “formal city”, increased in slums without interventions, and decreased in slums with interventions. BH-Viva represents an effort at advancing methodological issues, providing learning and theoretical backing for urban health research and research methods, allowing their application and extension to other urban contexts.