The second part of the assessment and evaluation of the unstructured-mesh Finite-volumE Sea ice–Ocean Model version 2.0 (FESOM2.0) is presented. It focuses on the performance of partial cells and embedded sea ice and the effect of mixing parameterisations available through the Community Vertical Mixing (CVMix) package. It is shown that partial cells and embedded sea ice lead to significant improvements in the representation of the Gulf Stream and North Atlantic Current and the circulation of the Arctic Ocean. In addition to the already existing Pacanowski and Phillander (fesom_PP) and K-profile (fesom_KPP) parameterisations for vertical mixing in FESOM2.0, we document the impact of several mixing parameterisations from the CVMix project library. Among them are the CVMix versions of Pacanowski and Phillander (cvmix_PP) and K-profile (cvmix_KPP) parameterisations; the tidal mixing parameterisation (cvmix_TIDAL); a vertical mixing parameterisation based on turbulent kinetic energy (cvmix_TKE); and a combination of cvmix_TKE and the recent scheme for the computation of the Internal Wave Dissipation, Energy, and Mixing (IDEMIX) parameterisation. IDEMIX parameterises the redistribution of internal wave energy through wave propagation, non-linear interactions and the associated imprint on the vertical background diffusivity. Further, the benefit from using a parameterisation of Southern Hemisphere sea ice melt season mixing in the surface layer (MOMIX) for reducing Southern Ocean hydrographic biases in FESOM2.0 is presented. We document the implementation of different model components and illustrate their behaviour. This paper serves primarily as a reference for FESOM users but is also useful to the broader modelling community.