Tropical Andean peatlands are home to a unique biodiversity and store large amounts of carbon. Mountain peatlands are frequent in the northern Andes and can cover up to 17% of the landscape. Although many mountain peatlands are small, covering one or few hectares, some can be large on unique geomorphic settings such as old lakes and abandoned volcanic craters. Peatlands develop in relatively flat areas, many of which have been transformed to agricultural fields after draining. Peatland drainage exposes organic matter to oxygen, increasing decomposition and C emissions. Methane emissions are controlled by vegetation, quality of the organic matter, temperature, and water table depth that affects degree of peat anoxia. They tend to be lower in mountain peatlands than lowlands, but few data exist. Our research focused on understanding the patterns of greenhouse gas fluxes on a large peatland in the central part of the Colombian Andes, including the variation on the main microtopographic features: hummocks, hollows and ditches. Half of the site was drained over 60 years ago, and a complex pattern of vegetation change, subsidence and flooding developed. We monitored carbon dioxide and methane fluxes for one year on the disturbed and undisturbed areas. Our results showed a higher rate of ecosystem respiration on disturbed (1.5 µmol m-2 s-1) than on undisturbed sites (0.6 µmol m-2 s-1) with higher rates of emission from hummocks lacking vegetation in the disturbed area. Methane emissions were influenced by soil temperature and depth to the water table, with higher emissions on disturbed sites with high water table than undisturbed sites. Overall species composition was different between the two areas with shrub and large herbaceous plants encroaching on the disturbed area. Our results highlight the negative climatic impacts of human activities on Andean mountain peatlands and suggest restoration pathways that can reduce GHG emissions and help to protect valuable species.