Biological self-healing occurs by metabolically calcium carbonate (CaCO3) precipitating bacteria. However, the cementitious matrix is hostile, and it is necessary to create a favorable environment for the prolonged viability of the bacteria. In this context, this study aimed to evaluate the efficiency of three bacterial strains in the self-healing of cracks (Bacillus subtilis—AP91, Bacillus cf. subtilis—BS, and Bacillus cf. cereus—BC) incorporated into the mixing water of cementitious mortars with and without air admixture. After 1 and 7 days of curing, realistic cracks were induced in the 40 × 40 × 160 mm prismatic specimens’ central region. Compressive strength and flexural tensile strength tests and image analysis in optical stereomicroscope and SEM were performed at different control ages for specimens in wet curing. It was verified that the bacterial strain influences the self-healing performance, with better results for BS, with healing rates of 95.72% in cracks with a thickness of 1.58 mm. Incorporating air into the mixture proved favorable to self-healing, with rates up to 126% higher than the same variation without the additive. The studied process is a promising biotechnological solution for recovering micro-cracks in cement-based materials, potentially increasing the matrix’s durability and strength. © 2023, The Author(s), under exclusive licence to Springer Nature Switzerland AG.