In this study, the applicability of two bacteria-based healing agents (e.g., poly-lactic acid and polyhydroxyalkanoate) in blast furnace slag cement (BFSC) mortar has been assessed. An experimental campaign on the functional properties, self-healing capacity, freezing–thawing and carbonation resistance has been conducted in comparison with plain mortar (Ctrl). Due to the relatively low alkalinity of the mixture, the addition of poly-lactic acid healing agents (PLA) caused coarsening of the micro-structure, decrease of strength and did not improve the self-healing capacity of the material. Among other consequences, the mass loss due to the freezing–thawing of PLA specimens was about 5% higher than that of the Ctrl specimens. On the contrary, no detrimental effect of the mortar functional properties was measured when polyhydroxyalkanoate healing agents (AKD) were added. The self-healing capacity of AKD specimens was higher than that of the Ctrl specimens, reaching a maximum healed crack width of 559 µm after 168 days of self-healing, while it was 439 µm for the Ctrl specimens and 385 µm for PLA specimens. The air void content of the AKD mixture was 0.9% higher than that of the Ctrl, increasing its resistance against freezing–thawing cycles. This study aims to confirm the potential applicability of AKD particles as self-healing agents in low-alkaline cementitious mixtures.