The main focus of this research was the bio-stimulated healing of cracks in lime mortar samples (historical and newly designed). The investigation started from comprehensive characterisation of historical mortars, while in the next stage a compatible conservation mortar was designed and characterised, with special attention given to the contact zone formation between original and conservation mortars. The next step was the design of a bio-stimulating crack-sealing agent, a two-component liquid system: bacteria culture Sporosarcina pasteurii DSM 33 and nutrients. Both historical and conservation mortar samples were used in order to study their potentials for bio-stimulated surface-crack repair. The experiment lasted for 150 days, allowing the ureolytic bacteria Sporosarcina pasteurii DSM 33 to induce the precipitation of calcium carbonate into cracks and heal the damaged surface of the tested materials. The healing phenomenon was continuously monitored during a period of 150 days. Special attention was given to the evaluation of the morphology, chemical and structural characteristics of the deposits created in/on the surface cracks, monitored by optical microscopy, SEM, XRF and XRD analyses. The obtained results present valuable input for the application of the developed system in real environmental conditions as a solution for the future sustainable architectural conservation of traditionally prepared mortars.