Anthropogenic forest disturbance and land use change (LUC) in the Amazon region is the main source of greenhouse gas emissions to the atmosphere in Brazil, due to the carbon (C) and nitrogen (N) emitted from vegetation clearance. Land use conversion associated with management practices plays a key role in the distribution and origin of C in different soil organic matter (SOM) fractions. Here, we show how changing land use systems have influenced soil C and N stocks, SOM physical fractions, and the origin of SOM in the Santarém region of the eastern Brazilian Amazon. Soil C and N stocks were calculated for the surface layer of 0–30 cm. Anthropogenic disturbances to the standing forest, such as selective logging and wildfires, led to significant declines in soil C and N stocks. However, in the long-term, the conversion of the Amazon forest to pasture did not have a noticeable effect on soil C and N stocks, presumably because of additional inputs from pasture grasses. However, the conversion to cropland did lead to reductions in soil C and N content. According to the physical fractionation of SOM, LUC altered SOM quality, but silt and clay remained the combined fraction that contributed the most to soil C storage. Our results emphasize the importance of implementing more sustainable forest management systems, whilst also calling further attention to the need for fire monitoring systems, helping to ensure the resilience of C and N stocks and sequestration in forest soils; thereby contributing towards urgently needed ongoing efforts to mitigate climate change.