Sustainable vineyard management in the tropical semiarid Sao Francisco Valley requires practices that enhance carbon (C) and nitrogen (N) storage, aggregate stability, and microbial functionality, thereby reinforcing soil resilience. Here, we investigated the effects of fully organic and conventional fertilization regimes on soil aggregation, carbon and nitrogen stocks, enzyme activity, mycorrhizal fungal spores, and glomalin-associated stabilization down to 40 cm depth. Total soil C and N stocks were comparable between the two grapevine systems, exhibiting increases of 46 % and 125 %, respectively, relative to adjacent native vegetation. Organic fertilization preferentially stabilized total C and N within small macroaggregates, increasing these stocks by 427 % and 103 %, whereas conventional fertilization concentrated them near the surface. Under conventional fertilization, C accumulation in large macroaggregates was restricted to the 0-10 cm layer, reflecting rapid rootmediated aggregation dynamics. Moreover, organic fertilization enhanced beta-glucosidase activity and supported higher abundances of arbuscular mycorrhizal fungal spores and total glomalin in deeper layers, reinforcing aggregate stabilization and promoting long-term C protection. Conversely, conventional fertilization primarily triggered rapid topsoil aggregation, largely due to nutrient-rich inputs. Carbon preservation capacity and the soil quality index integrated these processes, demonstrating that organic fertilization fosters a more resilient and multifunctional soil system than conventional fertilization or native vegetation. Overall, our findings emphasize that organic fertilization promotes vertical retention of C and N within macroaggregates, where intra-aggregate biochemical activity and physical protection jointly sustain long-term soil integrity in semiarid vineyards.