Subsoils store the majority of terrestrial organic carbon, yet the stability of this vast reservoir under climate change remains a critical uncertainty. In this study, we investigated soil profiles across a continental-scale aridity gradient on the Mongolian Plateau to assess the vulnerability of deep soil carbon fractions. Our results reveal that subsoil mineral-associated organic carbon (MAOC), traditionally considered a stable sink, is surprisingly more sensitive to increasing aridity than the labile particulate organic carbon (POC) fraction. Structural equation modeling links this unexpected vulnerability to a fundamental vertical shift in carbon stabilization controls. Unlike topsoils, which are closely linked to abiotic variables, subsoil carbon stability is primarily correlated with microbial community attributes, specifically microbial biomass and fungal diversity. This suggests that subsoil carbon storage is a biotically mediated process highly responsive to environmental stress. We conclude that current conceptual models, which often assume the universal kinetic persistence of MAOC, may critically underestimate the potential for carbon loss from deep dryland soils, posing a risk of positive carbon-climate feedbacks as drylands expand globally.