In this study, a novel non-toxic, biodegradable bacteria-based healing agent known as alkanoate derivatives (AKD) derived from wastewater was investigated for its self-healing efficiency of the mortar specimens in comparison to the already-developed healing agents made of lactic acid derivatives (PLA). Mortar with different percentages of healing agent inclusions (2.6% and 5% w/w cement) have been evaluated in this study. To assess the self-healing improvements of the mortar incorporated bacteria-based bio-plastic healing agent's self-healing capacity, quantification of self-healing efficiency was performed at two different healing intervals of 28 and 56 days through optical determination of crack closure by stereomicroscope, recovery of water tightness by rapid water permeability test and determination of mass percentage increase of calcium carbonate by thermogravimetric analysis (TGA). The healing products formed in the cracks were analyzed by TGA and X-ray diffraction (XRD). Furthermore, a statistical analysis was performed to understand the variability in the crack width, water flow and the correlation of self-healing ratios between the stereomicroscope and permeability measurements. The results revealed that series containing the healing agents displayed a higher crack closure ratio compared to plain mortar series for initial crack widths greater than 0.4 mm at 56 days of healing. Moreover, the recovery of water tightness for series containing bacteria were greater compared to plain mortar for initial crack widths greater than 0.6 mm at 56 days of healing. However, in healing agent incorporated mortar series, only alkanoate derivatives at 5% dosage reported an increase in mass % of calcium carbonate precipitation at 56 days of healing. From the statistical analysis, it was confirmed that the influence of internal crack geometry plays a significant role in the degree of healing and variation of the water flow for smaller crack widths as the healing period increases.