Microbially induced calcium carbonate precipitation (MICP) provides a biologically programmable route to fabricate functional composites; however, conventional strategies lack spatial control over mineral topology. This thesis explores mechanically directed MICP using a Lagrangian individual-based model (IbM) coupled with discrete element method (DEM) mechanics within the NUFEB framework. Microbial agents, extracellular polymeric substances (EPS), and mineral phases are modeled as deformable particles using the LAMMPS granular module with Verlet integration. Cellular growth, nutrient uptake, and urease production follow Monod kinetics and are coupled to local stress fields through mechanotransductive feedback. Advection–diffusion–reaction equations govern solute transport across an Eulerian voxel grid, coupling microbial activity to chemical gradients. The model simulates a hypothetical stress-responsive ureolytic bacterium that amplifies force asymmetries into anisotropic precipitation patterns, enabling the study of mechanotransduction-guided mineralization. External rigid-body constraints impose localized confinement and guide precipitation through template-assisted assembly. The results suggest that directional mineralization can emerge from coupled feedback between stress fields, reaction–diffusion dynamics, and microbial stress sensitivity. This work establishes a multiscale modeling foundation for programmable, stress-adaptive mineralization and highlights confinement geometry and mechanical feedback as tunable design parameters for self-structuring Engineered Living Materials (ELM).