The possible beneficial impact of self-healing on chloride transport through cracks has been assessed for two bacteria-based self-healing mortar mixtures in comparison with Ordinary Portland cement mortar. Intact self-healing specimens featured lower chloride transport coefficients thanks to a denser microstructure and to the formation of a layer of calcium carbonate on their surface. However, self-healing of cracks of cracked mortar specimens did not significantly reduce chloride penetration during 28 days of chloride exposure compared to cracked and non-healed specimens. On the other hand, this study demonstrated that self-healing of 150–200 µm wide cracks reduced chloride ingress during shorter term (14 days) chloride exposure in comparison to cracked but non-healed specimens. The results of this study suggest that self-healing of cracks through calcium carbonate formation results in water blockage (sealing) of cracks but that the limited amount of limestone formed creates an imperfect barrier against diffusion of chloride ions through the apparent porous limestone. The short-term positive effect of self-healing with respect to reduced chloride ingress could be beneficial in applications where chloride exposure is limited or non-permanent such as concrete structures irregularly exposed to deicing salts or located in the splash zone in marine environments.