Remote sensing and inverse modelling studies indicate that the tropics emit more CH4 and N2O than predicted by bottom-up emissions inventories, suggesting that terrestrial sources are stronger or more numerous than previously thought. Tropical uplands are a potentially large and important source of CH4 and N2O often overlooked by past empirical and modelling studies. To address this knowledge gap, we investigated spatial, temporal and environmental trends in CH4 and N2O fluxes across a~long elevation gradient (600–3700 m a.s.l.) in the Kosñipata Valley, in the southern Peruvian Andes that experiences seasonal fluctuations in rainfall. The aim of this work was to produce preliminary estimates of CH4 and N2O fluxes from representative habitats within this region, and to identify the proximate controls on soil CH4 and N2O dynamics. Ecosystems across this altitudinal gradient were both atmospheric sources and sinks of CH4 on an annual basis. Montane grasslands (or, puna; 3200–3700 m a.s.l.) were strong atmospheric sources, emitting 56.94 ± 7.81kg CH4-C ha−1 yr−1. Upper montane forest (2200–3200 m a.s.l.) and lower montane forest (1200–2200 m a.s.l.) were net atmospheric sinks (−2.99 ± 0.29 kg CH4-C ha−1 yr−1 and −2.34 ± 0.29 kg CH4-C ha−1 yr−1, respectively); while premontane forests (600–1200 m a.s.l.) fluctuated between source or sink depending on the season (wet season: 1.86 ± 1.50 CH4-C ha−1 yr−1; dry season: −1.17 ± 0.40 CH4-C ha−1 yr−1). Analysis of spatial, temporal and environmental trends in CH4 flux across the study site suggest that soil redox was a dominant control on net CH4 flux. CH4 emissions were greatest from elevations, landforms and during times of year when soils were sub-oxic, and CH4 efflux was inversely correlated with soil O2 concentration (r2 = 0.82, F1, 125 = 588.41, P < 0.0001). Ecosystems across the region were net atmospheric N2O sources. N2O fluxes declined with increasing elevation; N2O emissions from premontane forest, lower montane forest, upper montane forest and montane grasslands averaged 2.23 ± 1.31 kg N2O-N ha−1 yr−1, 1.68 ± 0.44 kg N2O-N ha−1 yr−1, 0.44 ± 0.47 kg N2O-N ha−1 yr−1 and 0.15 ± 1.10 kg N2O-N ha−1 yr−1, respectively. N2O fluxes from premontane and lower montane forests exceeded prior model predictions for the region. Comprehensive investigation of field and laboratory data collected in this study suggest that N2O fluxes from this region were primarily driven by denitrification; that nitrate (NO3−) availability was the principal constraint on N2O fluxes; and that soil moisture and water-filled porosity played a secondary role in modulating N2O emissions. Any current and future changes in N management or anthropogenic N deposition may cause shifts in net N2O fluxes from these tropical montane ecosystems, further enhancing this emission source.