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Investigating the enhanced mechanical response of treated soils through microbially induced calcite precipitation requires extensive understanding of the pore structure. Depending on the applied treatment conditions, the resulted material exhibits distinct changes in the solid phase. In this paper, we focus on the microstructural characteristics of bio-cemented soils derived from different treatment patterns. The objective is to clarify the predominant fabric features in function of the adopted treatment conditions. For this purpose, microstructural observations with Scanning Electron Microscopy (SEM) are used to analyse the structure during the treatment and post-treatment. Mesocrystals, i.e., aggregates of single particles, are identified as a distinct form of precipitate that provides the crucial grain-to-grain contact surfaces. The cemented samples are subsequently subjected to undrained triaxial shear test to investigate the response in three typical cases of bio-cemented samples produced at laboratory conditions: (i) one of very low calcite content (2.5% w/w), (ii) one with inhomogeneous distribution of calcite and (iii) for the case of homogenously distributed calcite mass. Improved characteristics are obtained in all three cases.