Nowadays, understory vegetation along the tree row is considered a vital source of agroecosystem services and functional biodiversity improvement in the fruit orchard. Hence, current orchard floor management systems encourage practicing a more sustainable approach that supports vegetation cover rather than keeping bare soil herbicide use, or tillage. A two-year field trial was conducted using two different ground management techniques; integrated mowing (mower and brush or disc) and herbicide (glyphosate) in two commercial apple and peach orchards in a nitrogen vulnerable zone (NVZ) of the Marche region, Italy. This study aimed to evaluate the effects of these practices on soil N status, weed abundance, percent of soil cover, and dry weed biomass production. Weed management systems had no significant effect on soil organic matter and N availability; however, an improvement was noticed under integrated mowing when compared to the one treated with herbicides. Integrated mowing had a significant effect on species richness, soil coverage, and weed biomass production, which was approximately 2-times higher than in the herbicide-treated plots. The overall results showed that integrated mowing maintained a balance in the soil N status of both orchards, while supporting above-ground weed biodiversity and soil protection.