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Fire emissions associated with land cover change and land management contribute to the concentrations of atmospheric pollutants, which can affect regional air quality and climate. Mitigating these impacts requires a comprehensive understanding of the relationship between fires and different land cover change trajectories and land management strategies. We develop future fire emissions inventories from 2010–2030 for Sumatra and Kalimantan (Indonesian Borneo) to assess the impact of varying levels of forest and peatland conservation on air quality in Equatorial Asia. To compile these inventories, we combine detailed land cover information from published maps of forest extent, satellite fire radiative power observations, fire emissions from the Global Fire Emissions Database, and spatially explicit future land cover projections using a land cover change model. We apply the sensitivities of mean smoke concentrations to Indonesian fire emissions, calculated by the GEOS-Chem adjoint model, to our scenario-based future fire emissions inventories to quantify the different impacts of fires on surface air quality across Equatorial Asia. We find that public health impacts are highly sensitive to the location of fires, with emissions from Sumatra contributing more to smoke concentrations at population centers across the region than Kalimantan, which had higher emissions by more than a factor of two. Compared to business-as-usual projections, protecting peatlands from fires reduces smoke concentrations in the cities of Singapore and Palembang by 70% and 40%, and by 60% for the Equatorial Asian region, weighted by the population in each grid cell. Our results indicate the importance of focusing conservation priorities on protecting both forested (intact or logged) peatlands and non-forested peatlands from fire, even after considering potential leakage of deforestation pressure to other areas, in order to limit the impact of fire emissions on atmospheric smoke concentrations and subsequent health effects.