The soils of Mediterranean semiarid environments are commonly characterized by low levels of organic matter and mineral elements, as well as severe weed infestations, which, taken together, cause an intensive use of auxiliary inputs (tillage, fertilizers, herbicides). Although cover crops are recognized to sustainably improve soil health, the impact of Trifolium subterraneum L. cover cropping needs specific attention. This research investigates for the first time the effects over 4 years of T. subterraneum and spontaneous flora cover crops, after either incorporating their dead mulches into the soil or leaving them on the soil surface, on soil organic matter (SOM), macroelements, mineral nitrogen, microelements, and weed seedbank dynamics as indicators of soil quality in an apricot orchard. Compared to a conventional management control, the T. subterraneum cover crop with the burying of dead mulch into the soil increased the amount of SOM (+ 15%), ammoniacal (+ 194%) and nitric (+ 308%) nitrogen, assimilable P2O5 (+ 5%), exchangeable K2O (+ 14%), exchangeable Na (+ 32%), exchangeable K (+ 16%), Fe (+ 15%), Mn (+ 28%), Zn (+ 36%), and Cu (+ 24%), while it decreased the weed seedbank size (‒ 54%) and enhanced weed biodiversity. These findings suggest that T. subterraneum cover cropping may be an environment-friendly tool to enhance soil quality and limit auxiliary input supply in Mediterranean orchards.