The transformation of natural ecosystems to intensive agriculture is one of the drivers of topsoil acidification. However, the extent of soil acidification throughout soil profile following land-use transformation remains insufficiently understood and poorly documented. To quantify the impacts of this land-use transformation, we conducted a paired-site investigation in southern China, comparing soil profiles (0-500 cm) from natural forests and adjacent intensively managed pomelo orchards. Within these profiles, we analyzed soil pH, exchangeable cations, and inorganic nitrogen forms, and employed statistical models to identify key drivers. Results indicated that the transformation of natural forests to pomelo orchards induced severe acidification across the entire 500 cm soil profile, with the most pronounced pH reduction (19.6%) occurring in the subsoil (160–180 cm). Paradoxically, despite this widespread acidification, exchangeable base cations (K +, Ca 2+, Mg 2+) were significantly enriched in the top 250 cm of orchard soils. Notably, soil NO 3 --N concentrations in pomelo orchards exceeded those in natural forest at all depths, while NH 4 +-N concentrations did not differ significantly between the two land-use systems. Correlation analysis revealed that soil pH in pomelo orchards had a stronger association with NO 3 --N. Clustering and partial least squares regression analysis further suggested that significant soil acidification occurred in the 0–250 cm soil layer due to NO 3 --N leaching from pomelo orchard cultivation. It can be seen that in intensive pomelo orchards, nitrogen-driven acidification overrides the ameliorative effect of base cation inputs, leading to a systemic and deep-seated acidification problem. Consequently, effective mitigation requires a shift from conventional topsoil management to integrated strategies that control nitrogen at the source and address the unique dynamics of the subsoil environment.