Soil organic carbon (SOC) is a mandatory pool in national inventory reports on greenhouse gas (GHG) emissions and removals to the UNFCCC. Hence, its accurate assessment is important. Modelling SOC changes for national GHG reports is encouraged, but the uncertainty related to this pool still presents a significant challenge; thus, verifying modelling results with field observations is essential. We used the process-based model Biome-BGCMuSo and assessed its suitability for use in Croatia’s GHG reporting. We modelled SOC stocks in the top 30 cm of the mineral soil layer (SOC₃₀) for four different land-use (LU) categories (Deciduous/Coniferous Forest, Grassland and Annual Cropland) distributed in three biogeographical regions (Alpine, Continental and Mediterranean) and compared them with results of a national soil survey. A total of 573 plot level simulations were undertaken and results were evaluated at three stratification levels (LU, LU × biogeographical region, and plot). The model reproduced the overall country mean of SOC₃₀ with no overall bias, and showed good performance at the LU level with no significant (p < 0.05) difference for all LUs except Deciduous Forest (11% overestimation). At finer stratifications, the model performance considerably worsened. Further model calibration, improvement and testing, as well as repeated soil survey are needed in order to assess the changes in SOC₃₀ and to evaluate the potential of the Biome-BGCMuSo model for use in GHG reporting.