Crack formation in concrete is one of the main reasons for concrete degradation. Calcium alginate capsules containing biological self-healing agents for cementitious materials were studied for the self-healing of cement paste and mortars through in vitro characterizations such as healing agent survivability and retention, material stability, and biomineralization, followed by in situ self-healing observation in pre-cracked cement paste and mortar specimens. Our results showed that bacterial spores fully survived the encapsulation process and would not leach out during cement mixing. Encapsulated bacteria precipitated CaCO3 when exposed to water, oxygen, and calcium under alkaline conditions by releasing CO32- ions into the cement environment. Capsule rupture is not required for the initiation of the healing process, but exposure to the right conditions are. After 56 days of wet-dry cycles, the capsules resulted in flexural strength regain as high as 39.6% for the cement mortar and 32.5% for the cement paste specimens. Full crack closure was observed at 28 days for cement mortars with the healing agents. The self-healing system acted as a biological CO32- pump that can keep the bio-agents retained, protected, and active for up to 56 days of wet-dry incubation. This promising self-healing strategy requires further research and optimization.