The contribution of different land-use systems in the humid tropics to increasing atmospheric trace gases has focused on forests, pastures, and crops with few measurements from managed, tree-based systems that dominate much of the landscape. This study from the Peruvian Amazon includes monthly nitrous oxide and methane fluxes from two cropping systems, three tree-based systems, and a 23-year secondary forest control. Average N2O fluxes from the cropping systems were two to three times higher than the secondary forest control (9.1 ¿g N m-2 h-1), while those of the tree-based systems were similar to the secondary forest. Increased fluxes in the cropping systems were attributed to N fertilization, while fluxes from the tree-based systems were related to litterfall N. Average CH4 consumption was reduced by up to half that of the secondary forest (-30.0 ¿g C m-2 h-1) in the tree-based and low-input cropping systems. There was net CH4 production in the high-input cropping system. This switch to net production was a result of increased bulk density and increased soil respiration resulting in anaerobic conditions. Reduced rates of N2O emissions, similar CH4 consumption, and high C sequestration rates in these tree-based systems compared with mature forests, coupled with the large area of these systems in the humid tropics, may partially offset the past effects of deforestation on increased atmospheric trace gas concentrations. In contrast, cropping systems with higher N2O emissions, substantially reduced CH4 consumption or even net CH4 emissions, and little C sequestration exacerbate those effects.