The Amazon forest is fire sensitive, but, where fires were uncommon as a natural disturbance, deforestation and drought are accelerating fire occurrences, which threaten the integrity of the tropical forest, the carbon cycle and air quality. Fire emissions depend on fuel amount and type, moisture conditions and burning behaviour. Higher-resolution satellite data have helped more accurately map global burnt areas; however, the effects of fuels on the combustion process and on the composition of fire emissions remain uncertain in current fire emissions inventories. By using multiple Earth observation-based approaches, here we show that total fire emissions in the Amazon and Cerrado biomes are dominated by smouldering combustion of woody debris. The representation of woody debris and surface litter presents a critical uncertainty in fire emissions inventories and global vegetation models. For the fire season 1 August to 31 October 2020, for which all approaches are available, we found 372277605Tg (median and range across approaches) of dry matter burnt, corresponding to carbon monoxide emissions of 39.12759Tg. Our results emphasize how Earth observation approaches for fuel and fire dynamics and of atmospheric trace gases reduce uncertainties of fire emission estimates. The findings enable diagnosing the representation of fuels, wildfire combustion and its effects on atmospheric composition and the carbon cycle in global vegetation–fire models.