Subsoils contain large amounts of organic carbon which is generally believed to be highly stable when compared with surface soils. We investigated subsurface organic carbon storage and dynamics by analysing organic carbon concentrations, fractions and isotopic values in 78 samples from 12 sites under different land-uses and climates in eastern Australia. Despite radiocarbon ages of several millennia in subsoils, contrasting native systems with agriculturally managed systems revealed that subsurface organic carbon is reactive on decadal timeframes to land-use change, which leads to large losses of young carbon down the entire soil profile. Our results indicate that organic carbon storage in soils is input driven down the whole profile, challenging the concept of subsoils as a repository of stable organic carbon.