Soil organic carbon (SOC) is the largest terrestrial carbon (C) stock, and the capacity of soils to preserve organic C (OC) varies with many factors, including land use, soil type, and soil depth. We investigated the effect of land use change on soil particulate organic matter (POM) and mineral-associated organic matter (MOM). Surface (0−10 cm) and subsurface (60−70 cm) samples were collected from paired sites (native and cropped) of four contrasting soils. Bulk soils were separated into POM and MOM fractions, which were analyzed for mineralogy, OC, nitrogen, isotopic signatures, and 14C. The POM fractions of surface soils were relatively unaffected by land use change, possibly because of the continuous input of crop residues, whereas the POM fractions in corresponding subsurface soils lost more OC. In surface soils, MOM fractions dominated by the oxides of iron and aluminum (oxide-OM) lost more OC than those dominated by phyllosilicates and quartz, which was attributed to diverse organic matter (OM) input and the extent of OC saturation limit of soils. In contrast, oxide-OM fractions were less affected than the other two MOM fractions in the subsurface soils, possibly due to OC protection via organo-mineral associations. The deviations in isotopic signature (linked with vegetation) across the fractions suggested that fresh crop residues constituted the bulk of OM in surface soils (supported by greater 14C). Increased isotopic signatures and lower 14C in subsurface MOM fractions suggested the association of more microbially processed, aged OC with oxide-OM fractions than with the other MOM fractions. The results reveal that the quantity and quality of OC after land use change is influenced by the nature of C input in surface soils and by mineral-organic association in subsurface soils.