Wet organic-rich mineral and peat soils in the tropical Andes represent a potentially significant, but little studied, source of methane to the atmosphere. Here we report the results of field and laboratory measurements of soil–atmosphere methane exchange and associated environmental variables from freely draining upland and inundation prone wetland soils in a humid puna ecosystem in the Southeastern Andes of Peru. Between seasons and across the landscape soil–atmosphere exchange varied between uptake and emission. Notable hotspots of methane emission, peaking during the wet season, were observed from both upland and wetland soils with particularly strong emissions from moss-accumulating topographic lows. This variability was best explained by the influence of oxygen concentration on methane production in superficial soil horizons.