Purpose Alley cropping systems introduce herbaceous strips planted with trees into cropped fields. While such systems may have a positive effect on soil fertility, the respective roles of the trees and the herbaceous vegetation in shaping this effect remain unclear. We investigated the effect of the distance from herbaceous strips with or without walnut trees on soil fertility and earthworm communities in a 20 year old Mediterranean plot intercropped with tomatoes. Methods We determined the effects of i) the presence of trees, ii) the distance from the herbaceous strip (0 m, 1 m and 2.5 m) and iii) the distance from the tree on microbial biomass and respiration, earthworm density and soil C, N and P contents in the 0–25 cm layer at three sampling seasons. Results Herbaceous strips presented a higher microbial biomass C related to soil organic carbon, a lower microbial metabolic quotient, and a higher density of earthworms than the crop alley regardless of tree presence. Soil organic carbon content increased in the presence of trees. Available P and microbial biomass increased at 1 m from the tree in the HS. Earthworm density and microbial biomass were higher at 1 m than at 2.5 m from the HS. Conclusions Herbaceous strips were an effective shelter for earthworms and fostered a high and efficient microbial biomass throughout the year, with or without trees, probably due to diversified vegetation and no soil disturbance. The mechanisms by which these changes could impact the crop alley remain to be studied.