Terrestrial biogeochemical models are essential tools to quantify climate-carbon cycle feedback and plant-soil relations from local to global scale. In this study, a theoretical basis is provided for the latest version of the Biome-BGCMuSo biogeochemical model (version 6.2). Biome-BGCMuSo is a branch of the original Biome-BGC model with a large number of developments and structural changes. Earlier model versions performed poorly in terms of soil water content (SWC) dynamics in different environments. Moreover, lack of detailed nitrogen cycle representation was a major limitation of the model. Since problems associated with these internal drivers might influence the final results and parameter estimation, additional structural improvements were necessary. In this paper the improved soil hydrology as well as the soil carbon and nitrogen cycle calculation methods are described in detail. Capabilities of the Biome-BGCMuSo v6.2 model are demonstrated via case studies focusing on soil hydrology, soil nitrogen cycle, and soil organic carbon content estimation. Soil-hydrology-related results are compared to observation data from an experimental lysimeter station. The results indicate improved performance for Biome-BGCMuSo v6.2 compared to v4.0 (explained variance increased from 0.121 to 0.8 for SWC and from 0.084 to 0.46 for soil evaporation; bias changed from-0.047 to-0.007 m3m-3 for SWC and from-0.68 to-0.2 mmd-1 for soil evaporation). Simulations related to nitrogen balance and soil CO2 efflux were evaluated based on observations made in a long-term field experiment under crop rotation. The results indicated that the model is able to provide realistic nitrate content estimation for the topsoil. Soil nitrous oxide (N2O) efflux and soil respiration simulations were also realistic, with overall correspondence with the observations (for the N2O efflux simulation bias was between-0.13 and-0.1 mgNm-2d-1, and normalized root mean squared error (NRMSE) was 32.4 %-37.6 %; for CO2 efflux simulations bias was 0.04-0.17 gCm-2d-1, while NRMSE was 34.1 %-40.1 %). Sensitivity analysis and optimization of the decomposition scheme are presented to support practical application of the model. The improved version of Biome-BGCMuSo has the ability to provide more realistic soil hydrology representation as well as nitrification and denitrification process estimation, which represents a major milestone.