Global warming is promoted by anthropogenic CO2 emissions into the atmosphere, while at the same time it is partially mitigated by carbon sequestration by terrestrial ecosystems. However, improvement in the understanding and monitoring of belowground carbon processes is essential for evaluating strategies for carbon sequestration including quantification of carbon stores for credits. A system for non-destructive in situ carbon monitoring in soil, based on inelastic neutron scattering (INS), is described. The system can be operated in stationary or scanning mode and measures soil to depth of approximately 30 cm. There is a good agreement between results obtained from INS and standard chemical analysis of soil cores collected from the same study site.