The growing of bioenergy crops has been widely suggested as a key strategy in mitigating anthropogenic CO2 emissions. However, the full mitigation potential of these crops cannot be assessed without taking into account their effect on soil carbon (C) dynamics. Therefore, we analyzed the C dynamics through four soil depths under a 14-year-old Miscanthus plantation, established on former arable land. An adjacent arable field was used as a reference site. Combining soil organic matter (SOM) fractionation with 13C natural abundance analyses, we were able to trace the fate of Miscanthus-derived C in various physically protected soil fractions. Integrated through the whole soil profile, the total amount of soil organic carbon (SOC) was higher under Miscanthus than under arable crop, this difference was largely due to the input of new C. The C stock of the macroaggregates (M) under Miscanthus was significantly higher than those in the arable land. Additionally, the C content of the micro-within macroaggregates (mM) were higher in the Miscanthus soil as compared with the arable soil. Analysis of the intramicroaggregates particulate organic matter (POM) suggested that the increase C storage in mM under Miscanthus was caused by a decrease in disturbance of M. Thus, the difference in C content between the two land use systems is largely caused by soil C storage in physically protected SOM fractions. We conclude that when Miscanthus is planted on former arable land, the resulting increase in soil C storage contributes considerably to its CO2 mitigation potential.