Accelerating climate change and biodiversity loss calls for agricultural practices that can sustain productivity with lower greenhouse gas emissions while maintaining biodiversity. Biodiversity-friendly agricultural practices have been shown to increase earthworm populations, but according to a recent meta-analyses, earthworms could increase soil CO2 and N2O emissions by 33 and 42%, respectively. However, to date, many studies reported idiosyncratic and inconsistent effects of earthworms on greenhouse gases, indicating that the underlying mechanisms are not fully understood. Here we report the effects of earthworms (anecic, endogeic and their combination) with or without plants on CO2 and N2O emissions in the presence of soil-moisture fluctuations from a mesocosms experiment. The experimental set-up was explicitly designed to account for the engineering effect of earthworms (i.e. burrowing) and investigate the consequences on soil macroporosity, soil water dynamic, and microbial activity. We found that plants reduced N2O emissions by 19.80% and that relative to the no earthworm control, the cumulative N2O emissions were 17.04, 34.59 and 44.81% lower in the anecic, both species and endogeic species, respectively. CO2 emissions were not significantly affected by the plants or earthworms but depended on the interaction between earthworms and soil water content, an interaction that was also observed for the N2O emissions. Soil porosity variables measured by X-ray tomography suggest that the earthworm effects on CO2 and N2O emissions were mediated by the burrowing patterns affecting the soil aeration and water status. N2O emissions decreased with the volume occupied by macropores in the deeper soil layer, whereas CO2 emissions decreased with the macropore volume in the top soil layer. This study suggests that experimental setups without plants and in containers where the earthworm soil engineering effects via burrowing and casting on soil water status are minimized may be responsible, at least in part, for the reported positive earthworm effects on greenhouse gases.