A multi-disciplinary approach is adopted in the present work towards investigating bio-cemented geo-materials which extends from sample preparation, to microstructural inspection and mechanical behaviour characterization. We suggest a new way to induce “cell-free” soil bio-cementation along with a comprehensive description of bio-improved mechanical and microstructural properties. We utilize the soil bacterium Sporosarcina Pasteurii in freeze-dried, powder -instead of vegetative-, state and determine overall reaction rates of “cell-free” Microbial-Induced Calcite (CaCO3) Precipitation (MICP). We further investigate strength and stiffness parameters of three base geo-materials which are subjected to MICP under identical external bio- treatment conditions. Different trends in the mechanical response under unconfined and drained triaxial compression are obtained for fine-, medium- and coarse-grained sands for similar range of final CaCO3 contents. Pre- and post-yield dilatancy-stress relationships are obtained revealing the contribution of dilatancy in the achievement of peak strength. Medium-grained sand yields higher dilatancy rates and increased peak strength with respect to fine-grained sand. Further, insight into the bio-cemented material’s fabric is provided through scanning electron microscopy, time-lapse video microscopy and X-ray micro-computed tomography with subsequent 3D reconstruction of the solid matrix. A qualitative description of the observed precipitation behaviours is coupled with quantified microscopic data referring to the number, sizes, orientations and purity of CaCO3 crystals. Results reveal that MICP adapts differently to the adopted base materials. Crystalline particles are found to grow bigger in the medium-grained base material and yield more homogenous spatial distributions. Finally, a new workflow is suggested to ultimately determine the crucial contact surface between calcite bonds and soil grains through image processing and 3D volume reconstruction.