Microbially Induced Calcite Precipitation (MICP) is a promising and sustainable soil improvement technique that enhances stiffness and strength through calcite cementation while largely preserving permeability. Grain-scale tensile and shear experiments on MICP-cemented glass beads have demonstrated that bond strength and failure modes are strongly governed by calcite morphology and the grain-cement interface, exhibiting debonding, internal fracture, and mixed failure mechanisms. To investigate these mechanisms numerically, a coupled material point-discrete element method (MP-DEM) framework was previously developed to model calcite bond damage between grains; however, this approach was limited to spherical particles. Natural soils exhibit inherently non-spherical particle geometries, quantified using elongation, flattening, roundness, and roughness indices, that significantly affect contact mechanics, cementation morphology, and the localization of damage. To account for these effects, the coupled framework is extended by employing a Level-Set Discrete Element Method (LS-DEM) to explicitly represent non-spherical soil particle geometries, while retaining the Material Point Method (MPM) to discretize calcite cementation and its damage evolution. The framework captures calcite as both a load-bearing cement and a damage-prone phase, with failure criteria based on bond degradation and anisotropic damage evolution, enabling assessment of how particle geometry and calcite precipitation morphology, including coating, meniscus, and flat filling, govern damage patterns and mechanical response in MICP-treated soils.