Tree planting on abandoned agricultural land could both restore the soil quality and increase the productivity of economically valuable woody species. Here, we assess the impact of mixed-species tree plantations on soil quality at a site in Central Italy where tree intercropping systems were established 20 years ago on a former agricultural land. These intercropping systems include two species of economic interest, Populus alba and Juglans regia, and one of three different nurse trees, i.e., Alnus cordata, Elaeagnus umbellata, both of which are N-fixing species, and Corylus avellana. We measured tree growth and compared how soil organic matter, soil extracellular enzymes, and nematodes of different feeding groups varied among the intercropping systems and relative to a conventional agricultural field. Our results indicate that tree plantation led to an increase in soil carbon and nitrogen, and enhanced enzyme activities, compared with the agricultural land. The proportion of nematode feeding groups was heterogeneous, but predators were absent from the agricultural soil. Multivariate analysis of soil properties, enzymatic activity, nematodes, and tree growth point to the importance of the presence N-fixing species, as the presence of A. cordata was linked to higher soil quality, and E. umbellata to growth of the associated valuable woody species. Our findings indicate that intercropping tree species provide a tool for both restoring fertility and improving soil quality.