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The quest for novel, performant materials and methods in the engineering practice is driven nowadays by the need to offer solutions to complex problems by coupling technical innovation with environmental responsibility. Such problems emerge in the geo-technical engineering field related to soil stabilization and rehabilitation applications. Especially in urban areas “good” soils are already taken and the remaining land often requires extensive soil strengthening works for securing the integrity of structures and mitigating risks related to failures and environmental threats. This thesis puts the focus on bio-mediated soil cementation, a technology which alters substantially the structure of geo-materials and endows them with improved overall mechanical behaviour. The technique integrates bacterial metabolic activity in soil-permeation solutions to induce the formation of calcite bonds in granular soils. In recent years, studies have found that altering biochemical treatment conditions affects the material’s mechanical response. However, the role of the intrinsic properties of the base material on the formation of the crystalline bond lattice remains underexplored. Moreover, the peculiar structure of bio-cemented soils has been previously addressed solely based on qualitative methods, via surface and textural observations, which provide only with limited insight into crucial fabric parameters that cannot be considered representative of the material at the macroscale. This research work introduces a new approach to experimentally characterize the behaviour of bio-cemented materials in light of quantitative evidence related to its micro-architecture. The goal is to go beyond established experimental approaches, by adopting a single treatment strategy for three different base materials and by providing with state-of-the-art determination of microscale parameters. To this purpose, a series of complementary micro-structural inspection tools are utilized and a workflow is established to estimate the crucial bond contact area. Distinctive precipitate behaviours are captured related to the geometries, morphologies and the number of active bonds in the 3D space. The main finding is that the average mass of bond content is not sufficient, as a parameter, for expressing the strength and stiffness of bio-treated geo-materials. The three different bio-cemented geo-materials are found to exhibit distinctive trends in their mechanical behaviour under unconfined and drained triaxial compression, for similar final bond contents. The obtained unconfined strength of medium-grained bio-cemented sand falls between 3 and 11.3 MPa for bond contents in the range of 5% to 10%. Contrary, fine-grained bio-cemented sand reaches approximately 2.6 MPa for similar bond contents. Another finding relates to an alternative method for microbial-induced calcite precipitation (MICP) via the ureolytic bacterium S. Pasteurii in freeze-dried form. The study of kinetics reveals that urea hydrolysis continues upon the complete breakdown of cell clusters. This confirms that the execution of MICP persists as a “cell-free” mechanism. This new application method can be seen as a preliminary step towards enhancing overall MICP reproducibility for mainstream geo-engineering applications. Therefore, the thesis provides with new understanding of: (i) factors affecting MICP efficiency, (ii) the peculiar micro-architecture of the bio-cemented material and (iii) its mechanical response.