Tree-based intercropping (TBI) systems have shown some promise in mitigating greenhouse gas emissions, such as by sequestering carbon and decreasing soil nitrous oxide emissions. However, the effects of TBI on soil methane fluxes remain unknown. In a field study, we failed to show differences in soil CH₄ production between TBI and conventional monocropping (CM) systems. Within TBI plots, however, we found significantly lower CH₄ concentrations near the middle of the alleys than closer to tree rows. Soil CH₄ concentrations also decreased with soil depth, even dipping below mean global atmospheric concentrations. Laboratory assays revealed a higher CH₄ oxidation potential in soils collected from TBI plots compared with CM plots. These assays also revealed a decrease in CH₄ oxidation potential after soils were amended with nitrate. We conclude that TBI could potentially reduce soil CH₄ emissions, whereas fertilizer nitrate may increase them.