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Graphical abstract, Measurements of greenhouse gas (GHG) fluxes, particularly methane (CH4) and nitrous oxide (N2O) in mountain ecosystems are scarce due to the complexity and unpredictable behavior of these gases, in addition to the remoteness of these ecosystems. In this context, we measured CO2, CH4, and N2O fluxes in four semi-natural pastures in the Pyrenees to investigate their magnitude and range of variability. Our interest was to study GHG phenomena at the patch-level, therefore we chose to measure the gas-exchange using a combination of a gas analyzer and manual chambers. The analyzer used is a photoacoustic field gas-monitor that allows multi-gas instantaneous measurements. After implementing quality control and corrections, data was of variable quality. We tackled this by categorizing data as to providing quantitative or only qualitative information: • 50% and 59% of all CH4 and N2O data, respectively, provided quantitative information above the detection limit. • We chose not to discard data providing only qualitative information, because they identify highest- and lowest-flux peak periods and indicate the variability of the fluxes, along different altitudes and under different climatic conditions. • We chose not to give fluxes below detection limit a quantitative value but to acknowledge them as values identifying periods with low fluxes.