Traditional soil management in vineyards and olive groves of semi-arid regions relies on repeated tillage, which accelerates soil organic matter (SOM) oxidation and limits long-term carbon storage. In the context of carbon-neutral agricultural strategies, understanding how alternative practices influence SOM stocks, redistribution, and stabilization is essential. We sampled six paired sites in central Spain (three vineyards and three olive groves), each comprising adjacent plots under conventional tillage or continuous cover cropping, at 0-10 and 10-30 cm depths. We analyzed water-extractable organic carbon (WEOC), optical properties of water-extractable organic matter (WEOM; specific UV absorbance at 254 nm (SUVA254) and the absorbance ratio E4/E6), beta-glucosidase activity, and the SOC/clay ratio as a proxy for mineral-associated SOC stabilization. Depth was the main factor structuring SOC and biological activity, with higher values in the topsoil. Management effects on bulk SOC were limited although cover cropping increased aboveground biomass and influenced WEOC dynamics. Vertical contrasts (30-10 cm) showed a positive association between WEOC and SOC/clay, suggesting that increased WEOC at depth co-varies with stabilization potential. Partial least squares analysis for 10-30 cm showed that SOC/clay was associated with WEOC, E4/E6, and beta-glucosidase activity. These results suggest that subsoil carbon stabilization in semi-arid conditions may be linked to DOC availability and microbial processing rather than directly to surface biomass inputs.