Soils are as yet the only biological sink for atmospheric methane, earth’s second most important greenhouse gas, and the methane uptake capacity of agricultural soils is substantially reduced compared to native soils. Using a new laser-diffraction analysis-based method, we show in an extensive field study a new relationship between soil aggregate stability, atmospheric methane uptake, and SOM. Soil organic matter content, which is steerable by using organic amendments like compost, increases soil aggregate stability, which enhances atmospheric soil methane uptake. These results provide a potential new strategy on atmospheric methane mitigation.