The objective of this study was to determine enteric methane (CH4) emissions from lactating cows grazing in two prevalent systems, cultivated pasture system (CU) or native pasture system (NA) in the high Andes of Peru. In CU, multiparous Brown Swiss cattle grazed alfalfa and oat pastures and were supplemented daily with 1 kg of concentrate per cow. In NA, primiparous crossbred cows grazed native pastures without supplementation. The same animals were used in the rainy and dry season for both grazing systems. The SF6 tracer technique was used to measure CH4 emissions. Faecal excretion was measured using titanium dioxide marker, organic matter digestibility was estimated from faecal crude protein concentration and both parameters were used to calculate daily feed intake. Individual milk yield was recorded and samples analysed for their composition. Higher organic matter digestibility was observed in CU than NA (660 vs. 612 g/kg OM; P < 0.001) and in rainy than dry season (653 vs. 619 g/kg OM; P < 0.001). For enteric CH4 emission expressed per unit of organic matter intake (OMI), CU had lower emission than NA (27.3 vs. 34 g/kg OMI; P < 0.001). Cultivated pasture system also presented lower enteric CH4 emission per digested OMI than NA (41.4 vs. 55.5 g/kg digested OMI; P < 0.001). Despite the above, no differences were observed between systems (P = 0.263; P = 0.34) or seasons (P = 0.058; P = 0.06) on methane yield (MY; g CH4/kg DMI) or CH4 conversion factor (Ym;% GE intake), averaging 24.7 (SE 1.07) and 7.88 (SE 0.34) across all treatments respectively. Intensity of CH4 emission (grams per unit of energy corrected milk yield) (MI) presented a system × season interaction (P < 0.001), where NA had higher MI than CU (102 vs. 26.9 g/kg ECM; P < 0.001) with higher estimates during the rainy season, but differences between rainy and dry season were much greater for the NA system. In the current experiment, there was a confounding effect of season with stage of lactation, and of grazing system with animal genotype and parity status of the cows, therefore, care must be taken in interpreting these results. Overall, the current results indicate that multiparous lactating cattle grazing on alfalfa and oats pastures have a significantly lesser methane emission per kg of ECM than primiparous lactating cattle grazing on natural pasture in the high Andes of Peru.