The self-sealing process, associated with chemical and microstructural changes inside damaged cement-based composites, leads to the recovery of the original material integrity. Assessing the magnitude of internal changes in samples using non-destructive techniques to capture only the self-sealing effects is difficult. The challenge is evaluating the differences between subsequent observations in time and between samples with different properties. This paper proposes a new approach to the use of an ultrasonic technique for self-sealing investigation. The method allows the quantification of material changes strictly related to self-sealing processes, excluding changes caused by the naturally progressing hydration of binders. The applied ultrasonic pulse velocity (UPV) data processing procedure allows the investigation of material changes inside and near the cracks, the effects of stimulating the self-sealing of cement composites with mineral additives, and the assessment of changes over time. An important aspect of the method is the sample preparation procedure and testing conditions that reduce the impact of moisture content on the UPV measurements. New parameters allowing the quantitative characterization of the self-sealing process are proposed. The method was evaluated using cement mortars modified with siliceous fly ash with induced cracks 0 to 750 µm wide, which were then cured in water for 152 days. The maximum degree of effective crack filling as a result of autogenous self-sealing in the tested mortars was determined to range from 33% to 57%. Observations of the microstructure of the crack surface confirmed that apart from the volume of the newly formed products, the density of these products may have a key impact on the ultrasonic measurements of the self-sealing performance. The studies were supplemented by the examination of the compression strength of mortars, mortar sample scanning and computer image processing, and observations using an optical microscope and scanning electron microscope with energy dispersive spectroscopy.