Little is known about the abundance and geochemical behaviour of gaseous methane in the unsaturated zone of karst terrains. The concentrations and δ13C of methane in background atmosphere, soil air and cave air collected at monthly intervals over a 4 yr period are reported for St. Michaels Cave, Gibraltar, where the regional climate, surface and cave processes are well documented. Methane concentrations measured in Gibraltar soil are lower than the local background atmosphere average of 1868 ppb and fall to <500 ppb. The abundance–δ13C relationships in soil air methane lack strong seasonality and suggest mixing between atmosphere and a 12C depleted residue after methanotrophic oxidation. Methane abundances in cave air are also lower than the local background atmosphere average but show strong seasonality that is related to ventilation-controlled annual cycles shown by CO2. Cave air methane abundances are lowest in the CO2-rich air that outflows from cave entrances during the winter and show strong inverse relationship between CH4 abundance and δ13C which is diagnostic of methanotrophy within the cave and unsaturated zone. Anomalies in the soil and cave air seasonal patterns characterised by transient elevated CH4 mixing ratios with δ13C values lower than −47‰ suggests intermittent biogenic input. Dynamically ventilated Gibraltar caves may act as a net sink for atmospheric methane.