With deforestation and associated fires ongoing at high rates, and amidst urgent need to preserve Amazonia, improving the understanding of biomass burning emissions drivers is essential. The use of orbital remote sensing data enables the estimate of both biomass burning emissions and deforestation. In this study, we have estimated emissions of particulate matter with diameter less than 2.5 µm (PM2.5) associated with biomass burning, a primary human health risk, using the Brazilian Biomass Burning emission model with Fire Radiative Power (3BEM_FRP), and estimated deforestation based on the MapBiomas dataset. Using these estimates, we have assessed for the first time how deforestation drove biomass burning emissions in Amazonia over the last two decades at three scales of analysis: Amazonia-wide, country/state and pixel. Amazonia accounted for 48% of PM2.5 emitted from biomass burning in South America and current deforestation rates have reached values on par with those of the early 21st Century. Emissions and deforestation were concentrated in the Eastern and Central-Southern portions of Amazonia. Amazonia-wide deforestation and emissions were linked through time (R = 0.65). Countries/states with the widest spread agriculture were less likely to be correlated at this scale, likely because of the importance of biomass burning in agricultural practices. Concentrated in regions of ongoing deforestation, in 18% of Amazonia grid cells PM2.5 emissions associated with biomass burning and deforestation were significantly positively correlated. Deforestation is an important driver of emissions in Amazonia but does not explain biomass burning alone. Therefore, future work must link climate and other non-deforestation drivers to completely understand biomass burning emissions in Amazonia. The advance of anthropogenic activities over forested areas, which ultimately leads to more fires and deforestation, is expected to continue, worsening a crisis of dangerous emissions.