Amazonia hosts the Earth’s largest tropical forests and has been shown to be an important carbon sink over recent decades. This carbon sink seems to be in decline, however, as a result of factors such as deforestation and climate change. Here we investigate Amazonia’s carbon budget and the main drivers responsible for its change into a carbon source. We performed 590 aircraft vertical profiling measurements of lower-tropospheric concentrations of carbon dioxide and carbon monoxide at four sites in Amazonia from 2010 to 2018. We find that total carbon emissions are greater in eastern Amazonia than in the western part, mostly as a result of spatial differences in carbon-monoxide-derived fire emissions. Southeastern Amazonia, in particular, acts as a net carbon source (total carbon flux minus fire emissions) to the atmosphere. Over the past 40 years, eastern Amazonia has been subjected to more deforestation, warming and moisture stress than the western part, especially during the dry season, with the southeast experiencing the strongest trends. We explore the effect of climate change and deforestation trends on carbon emissions at our study sites, and find that the intensification of the dry season and an increase in deforestation seem to promote ecosystem stress, increase in fire occurrence, and higher carbon emissions in the eastern Amazon. This is in line with recent studies that indicate an increase in tree mortality and a reduction in photosynthesis as a result of climatic changes across Amazonia.