Cracks in cement-based materials are a common issue to be solved in construction and civil engineering. Although in the last 20 years microbiologically induced carbonate precipitation (MICP) has been investigated successfully to recover and improve the physical properties of cracked concrete, the assessment of the effectiveness of treatments is a very important challenge to solve. In this article, a non-destructive methodology is reported to monitor the progress of crack sealing and calcium carbonate (calcite) deposition during MICP. An ureolytic bacteria was applied to treat mortar specimens for 30 wk, in which the effectiveness of calcite precipitation was evaluated. For this, two-dimensional X-ray tomography was used to characterize the calcite filling progress, showing that the MICP treatment had a higher CaCO3 filling effect when compared to control. It was estimated that MICP activity allowed to fill mortar holes with CaCO3 by 18–27%, after 8 wk. As a comparison indicator during repair treatments of cement-based materials using microorganisms that perform MICP, a Relative Treatment Effect (RTE) index was proposed. It is concluded that X-ray tomography can be used as an effective non-destructive technique to track the progress of MICP during calcite deposition and crack repair. HIGHLIGHTS An experimental study was carried out to monitor progression of mortar healing by ureolytic bacteria by non-destructive methods. X-ray tomography technology was feasible to monitor mortar healing in real time. Relative effect (RTE) is proposed as a comparison index in the repair treatments of cement-based materials by Microbiologically Induced Carbonate Precipitation (MICP).