The study presents a comprehensive characterization of the fabric of bio-improved soils by introducing an image based quantitative analysis of the crystalline bond lattice, as a means of better understanding and interpreting the observed mechanical response. Calcium carbonate (CaCO3) bonds, produced under the presence and metabolism of the soil bacterium Sporosarcina Pasteurii, are analyzed through micro-Computed Tomography (μ-CT). Using a digital-based image processing methodology, and subsequent three-dimensional reconstruction of the solid matrix, we determine the bond particle orientation, sizes and volumetric fraction. Such parameters referring to the morphology and spatial distribution of crystals have been treated so-far in the literature, mainly, in qualitative methods. The study presented herein provides with new insight into the irregular morphology of the crystalline bond lattice and the critical role of the contact area between soil particles and calcite nuclei. Results from fine- and medium-grained bio-improved sands are validated against experimentally measured parameters. CaCO3 bonds are found to exhibit distinctive morphological trends which affect the contact area and ultimately, the mechanical response of the bio-cemented geo-material.