In Europe, about 55% of concrete bridges are about 50 years old and require non-structural rapid repair strategies to reinstate the aesthetic and durability performances. Existing strategies focus primarily on superficial restoration that continues to demonstrate premature deterioration due to inevitable micro-crack formations that further propagate to macro-cracks leading to the ingress of moisture along with harmful ions. In this study, the benefits of self-healing technology to control moisture ingress at the microscale were investigated. For this, tailored microcapsule with inorganic healing agent, specifically, commercially available water-repellent agent (SIKAGARD 705L) was added to mortar with two types of commonly used binders namely CEMI 52.5N and CEMI 52.5R. The compatibility assessment in terms of capsule integration, fresh and hardened properties was done. The baseline healing efficiency of the mortars without any healing additions was obtained to understand the autogenous healing capacity of the reference mortars. Subsequently, the reference mortar mixes were compared with mixes containing varying fractions of microcapsules (3, 5, and 10%) for autonomous healing efficiency with capillary absorption as the main durability function. The healing efficiency was further investigated for two different crack mouth widths (<250 μm and >350 μm); representative of non-structural residual crack widths. In mortars with microcapsules, a maximum reduction of sorptivity coefficients up to 82% and 78% with CEMI 52.5N and CEMI 52.5R mortars, respectively, for specimens cracked after 7 days of curing was observed. Subsequently, a synergetic effect of autogenous healing action and autonomous water-repellent action for durability recovery was identified and proved useful for repair mortar applications. The healing agent investigated, capsule content, and healing environment considered in the current study lay a foundation for further optimisation to improve the performance and to suit different applications.