Earthworms are considered as key actors of soil processes at different spatial and temporal scales and provide essential ecosystem services linked to climate regulation or primary production. However, little is known about their basic functional roles (e.g. organic matter decomposition, soil structuring processes) in perturbed systems such as urban or alluvial soils. Alluvial soils are characterized by regular physical perturbation through flooding and associated erosion/sedimentation processes which are rather similar to perturbations (e.g. temporal instability, spatial heterogeneity) affecting urban soils. Due to their close soil characteristics, we hypothesized that in both cases, soil functioning is similar with respect to soil fauna activity. Under controlled conditions, our objective was to investigate the effects of two endogeic earthworm species, Allolobophora chlorotica (pink morph) and Aporrectodea rosea (the two most abundant species found in the studied urban site), on soil organic matter (SOM) dynamics and soil structure (network of earthworm burrows) comparing an urban and an alluvial soil. We investigated the growth of individuals (weight gain and reproduction success) and assessed their effects on SOM decomposition (cumulative C–CO2 emission, nitrogen and phosphorus mineralization) and soil structure (macroporosity, total length and connectivity of segments) after one and three months of incubation. Our results showed higher growth of A. rosea in the alluvial soil compared to the urban soil. However, the total length of burrows, carbon and nitrogen mineralization were often higher in the urban soil especially when the two species were combined. This trend can be mainly explained by lower organic matter content found in the urban soil which may influence positively the burrowing activity and negatively the growth of earthworms. Endogeic earthworms appear a key feature of the soil functioning in the urban context through their roles on organic matter transformation, the formation and maintenance of the soil structure.