In recent years, methane (CH4) has received increasing scientific attention because it is the most abundant non-CO2 atmospheric greenhouse gas (GHG) and controls numerous chemical reactions in the troposphere and stratosphere. However, there is much that is unknown about CH4 sources and sinks and their evolution over time. Here we show that near-surface cavities in the uppermost vadose zone are now actively removing atmospheric CH4. Through seasonal geochemical tracing of air in the atmosphere, soil and underground at diverse geographic and climatic locations in Spain, our results show that complete consumption of CH4 is favoured in the subsurface atmosphere under near vapour-saturation conditions and without significant intervention of methanotrophic bacteria. Overall, our results indicate that subterranean atmospheres may be acting as sinks for atmospheric CH4 on a daily scale. However, this terrestrial sink has not yet been considered in CH4 budget balances.