Soil organic carbon (SOC) and nitrogen (N) contents are controlled partly by plant inputs that can be manipulated in agricultural systems. Although SOC and N pools occur mainly in the topsoil (upper 0.30 m), there are often substantial pools in the subsoil that are commonly assumed to be stable. We tested the hypothesis that contrasting long-term management systems change the dynamics of SOC and N in the topsoil and subsoil (to 0.75 m) under temperate conditions. We used an established field experiment in the UK where control grassland was changed to arable (59 years before) and bare fallow (49 years before) systems. Losses of SOC and N were 65 and 61% under arable and 78 and 74% under fallow, respectively, in the upper 0.15 m when compared with the grass land soil, whereas at 0.3–0.6-m depth losses under arable and fallow were 41 and 22% and 52 and 35%, respectively. The stable isotopes 13C and 15N showed the effects of different treatments. Concentrations of long-chain n-alkanes C27, C29 and C31 were greater in soil under grass than under arable and fallow. The dynamics of SOC and N changed in both topsoil and subsoil on a decadal time-scale because of changes in the balance between inputs and turnover in perennial and annual systems. Isotopic and geochemical analyses suggested that fresh inputs and decomposition processes occur in the subsoil. There is a need to monitor and predict long-term changes in soil properties in the whole soil profile if soil is to be managed sustainably.