Soils of mountain regions are estimated to contain large amounts of organic matter (OM), equivalent to stocks found in high-latitude boreal and tundra soils. Mountain environments are also experiencing profound changes in land management under the influence of socio-economic pressures as well as the need to adapt to climate change, which is occurring at a faster rate than in lowland areas. These anthropogenic impacts are expected to strongly affect soil OM storage. Most studies of land-use change have however focused on topsoil OM; whether similar trends will hold true for subsoil OM remains unknown. Using Rock-Eval pyrolysis as a proxy for soil OM dynamics, we showed that the hierarchy of controls on OM properties and transformations varied greatly with increasing soil depth. In the topsoil, OM properties were related to the nature of plant inputs, their degree of in-mixing with the mineral matrix and the occurrence of seasonal water saturation. In the subsoil however, the foremost predictors of OM properties were geochemical parameters. This shift in the nature of determinants of OM dynamics indicates that shallow and deep soil OM pools should respond differently to external forcings. Podzolic profiles showed the strongest decoupling of topsoil and subsoil OM properties. We focused on this soil type to specifically investigate the effects of land use on subsoil OM. We selected field sites from the Coastal Range of British Columbia, Canada and the Pennine Alps, Switzerland representing undisturbed and managed forest, shrubland and pasture. Samples were analyzed for organic C content, OM quality and reactive mineralogy. Results showed that herbaceous cover was associated with an increase in topsoil but not subsoil OM. In the subsoil, variations in OM content and properties were associated with changes in reactive Al and Fe mineral phases. Overall, our data indicate that organo-mineral and organo-metal interactions are of prime importance to OM accumulation in the subsoil, and that understanding the response of deep soil C stocks to land use change will require consideration of the geochemical and mineralogical environment. Our results further suggest that so-called reactive mineral phases may themselves be impacted by land use, in turn affecting deep soil C stabilization and destabilization processes.