With the development of cracks on their surfaces, mortar’s service life dramatically shortens. Self-healing concrete by Microbiologically Induced Calcite Precipitation (MICP) is one of the high-tech concretes being used to address these issues. This type of mortar can start biological processes to repair itself and deal with its cracks. The self-healing effectiveness of two different bacteria, in this paper, Bacillus subtilis and Bacillus cereus, added to the mortar is examined experimentally. In order to conduct this investigation, artificial cracks were made in the mortar. A 3D optical microscope was used to take repeated pictures of the cracked mortar. The mechanical and durability tests conducted on the bacterial mortar were used to gauge the efficacy of self-healing. Mortar samples were left for 7, 14, and 28 days to cure. Compressive strength, flexural strength, water absorption, and sorptivity were measured during various times of the curing process. The test results showed that the mortar with bacteria had an increase in strength and durability compared to the control mix. In the sample of mortar containing bacteria, Bacillus subtilis and Bacillus cereus a maximum increase of 17.29% and 11.31% in flexural strength, 17.77% and 12.84% in compressive strength were observed and a 34.48% and 26.43% decrease in water absorption in the mortar sample containing bacteria, Bacillus subtilis and Bacillus cereus at 28 days, respectively. The results of the mortar absorption test showed that the addition of bacteria to the mortar matrix significantly reduced the primary and secondary absorption rates of bacterial mortars B-M-1 and B-M-2. Using a 3D light microscope, the cracks in the bacterial mortar showed that larger amounts of white crystal precipitates were generated that nearly filled the surface of the crack. Overall, Bacillus subtilis appeared to be superior to Bacillus cereus based on the results of mechanical and mortar durability tests because calcium carbonate precipitates more rapidly.