Soil organic matter (SOM) can be characterised by soil organic carbon (SOC) and/or total nitrogen (TN). The observed dynamics of SOC and TN in the topsoil of a 28-year-old fallow experiment on Haplic Chernozem was modelled using the Candy Carbon Balance (CCB) model. This study selected two treatments from this experiment where the soil was kept bare with mechanical or chemical (herbicides) treatments. The CCB model was improved to include the SOC related change of soil physical parameters and dynamic handling of the physically stabilised SOM pool. Over 28 years of bare fallow the top soil lost about 10 t/ha of SOC and > 1 t/ha of TN. The results from observation and modelling reflected the increased SOM turnover due to soil tillage. The modelled size of the physically stabilised SOC pool was about 55% of total SOC and only reduced slowly during the almost three decades, but the implementation of this effect improved simulation results and reduced the relative RMSD (unitless) from 0.051 to 0.044 for SOC and from 0.053 to 0.049 for TN error level. From these results we conclude that the larger the SOM change the more important is the integration of the turnover of physically stabilised SOM within the modelling approach.