The soils of tropical montane forests can act as sources or sinks of atmospheric methane (CH4). Understanding this activity is important in regional atmospheric CH4 budgets given that these ecosystems account for substantial portions of the landscape in mountainous areas like the Andes. We investigated the drivers of net CH4 fluxes from premontane, lower and upper montane forests, experiencing a seasonal climate, in south-eastern Peru. Between February 2011 and June 2013, these soils all functioned as net sinks for atmospheric CH4. Mean (standard error) net CH4 fluxes for the dry and wet season were −1.6 (0.1) and −1.1 (0.1) mg CH4-C m−2 d−1 in the upper montane forest, −1.1 (0.1) and −1.0 (0.1) mg CH4-C m−2 d−1 in the lower montane forest, and −0.2 (0.1) and −0.1 (0.1) mg CH4-C m−2 d−1 in the premontane forest. Seasonality in CH4 exchange varied among forest types with increased dry season CH4 uptake only apparent in the upper montane forest. Variation across these forests was best explained by available nitrate and water-filled pore space indicating that nitrate inhibition of oxidation or diffusional constraints imposed by changes in water-filled pore space on methanotrophic communities may represent important controls on soil–atmosphere CH4 exchange. Net CH4 flux was inversely related to elevation; a pattern that differs to that observed in Ecuador, the only other extant study site of soil–atmosphere CH4 exchange in the tropical Andes. This may result from differences in rainfall patterns between the regions, suggesting that attention should be paid to the role of rainfall and soil moisture dynamics in modulating CH4 uptake by the organic-rich soils typical of high-elevation tropical forests.