Bio-cementation through microbially induced calcite precipitation (MICP) has the potential to overcome several technical and environmental limitations of conventional cement-based soil improvement techniques. While a significant amount of research has been directed towards better understanding and controlling MICP processes, there is still a lack of multiphysical formulations that can be used for the design of real geotechnical applications in which both the treatment extent and its strength and deformability need to be evaluated. This paper presents the development and application of a comprehensive bio-chemo-hydro-mechanical model that can be used for designing MICP treatments with the finite element method. To overcome the limitations of current approaches based on elasticity, the formulation involves an elastoplastic constitutive model based on Mohr-Coulomb that can predict the strength increase of MICP-improved soils. The model can easily be calibrated with existing experimental results. The scope of model application is demonstrated through the case of a 2D shallow foundation strengthening. Results reveal that the questions of what level of cementation to target and how to distribute cementation efficiently are of equal importance to ultimately serve the needs of specific geotechnical problems, such as those of bearing capacity.