In temperate Europe, agroforestry practice is gaining interest due to its potential to enhance carbon (C) sequestration and mitigate greenhouse gas (GHG) emissions in agriculture. To date, the effects of agroforestry on the spatial and temporal dynamics of soil carbon dioxide (CO2) and methane (CH4) fluxes are still poorly quantified. Here we present a systematic comparison of soil CO2 and CH4 fluxes between agroforestry and monoculture cropland systems for the first time, based on two-year field measurements at three sites on different soils in Germany. Each site had an adjacent alley cropping agroforestry system and monoculture, and the agroforestry was established on former monoculture croplands 1 to 11 years prior to this study. We found that area-weighted soil CO2 emissions from agroforestry (3.5−8.1 Mg C ha−1 yr−1) were comparable to monocultures (3.4−9.8 Mg C ha−1 yr−1), whereas area-weighted agroforestry generally had higher soil CH4 uptake (0.4−1.3 kg C ha−1 yr−1) compared to monocultures (0.1−1.2 kg C ha−1 yr−1). Seasonal variations of soil CO2 and CH4 fluxes were strongly regulated by soil temperature and moisture, and the spatial variations were influenced by soil texture. Our results suggest that conversion of monoculture cropland to long-term alley cropping agroforestry system could be considered as a sustainable agriculture practice for its great potential for mitigating CH4 emissions.