The characterisation of lime mortars is a relevant task for the conservation of ancient buildings and the correct design of repair materials; among the relevant properties to be studied, the pore structure stand out, which is influenced by the manufacturing processes, receipts and technical expedients and is related to the strength and durability of the mortars. Among other things, the ancient practice of fermenting organic matter in water and adding it to the lime mixture has shown great potential for improving workability and mechanical performance of the building environment. In fact, this practice ensures an internal source of forced carbonation, which in turn determines the precipitation of new mineral phases and the efficient modification of the pore structure. However, a full understanding of the contribution of organically fermented water in lime mortars requires a detailed visual inspection. In this respect, the use of high-resolution synchrotron radiation computed microtomography (SR-μ-CT) proves to be an effective tool for the validation of volumetric data and the three-dimensional representation of studied objects. Under these premises, SR-μ-CT has been used to study different mortars prepared by fermenting various organics in the mixing water. The combination of 3D imaging and traditional physical-mechanical characterisation tests supported the modelling of forced carbonation induced by organically fermented water, suggesting that the different proportions in carbohydrates, fats and proteins of selected organics influence the final pore architecture and mechanical properties of the mixtures since the first phases of carbonation. In particular, carbohydrate-rich organics promote the development of a uniform microstructure and improved mechanical strength, whereas fat-rich organics determine a different and less efficient microstructure due to the low carbonation reactions, the major contribution of larger pores and the lower connectivity between them.