When deforestation is followed by continuous arable cropping, a permanent decline of between 22% and 42% in the soil organic carbon (SOC) has been reported. This systematic loss of soil carbon (C) is mainly attributed to the loss of physically protected SOC. The Rothamsted Carbon model (RothC) does not include a description of the processes of physical protection of SOC and so losses of C during continuous cultivation of previously uncultivated land are not likely to be accurately simulated. Our results show that in the first years following deforestation, RothC does not capture the fast drop in forest derived soil C. However, the model does satisfactorily simulate the changes in SOC derived from the following crops. Uncertainty in input data and accounting for erosion, does not explain the underestimation of decomposition after deforestation by RothC. A simple approach to increase decomposition by multiplying rate constants is evaluated. This approach needs high multiplication rates and leads to an overestimation of plant input values to sustain SOC equilibrium levels. However, the ability of RothC to simulate changes in the forest derived SOC can be greatly improved with an implementation of a simple approach to account for SOC dynamics due to the loss of physically protected C. This approach implements a new soil carbon pool into RothC which represents the labile but protected carbon fraction which builds up under minimally disturbed land uses, and which loses its protection once the soil is disturbed. The new pool is calibrated using 13C natural abundance analysis in conjunction with soil fractionation.