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Biologically self-healing concretes are generally composed of immobilized or encapsulated bacterial spores and nutrients. The efficiency of this self-healing approach depends on the effective protection and storage by the carriers. This report describes a novel sustained-release strategy for the improved self-healing function and microcapsule resistance to the cement environment. Halloysite clay nanotubes (HNTs) loaded with the common microbiological nutrient, yeast extract (YE) were encapsulated in calcium alginate microcapsules alongside Bacillus pseudofirmus spores. The encapsulation of the YE-loaded HNTs improved the resistance of the microcapsules to the cement environment, improved the microcapsule-cement interface, while successfully retaining the nutrients after direct contact with the cement pore solution. The self-healing system effectively healed artificial concrete cracks compared to control samples, reducing the crack water tightness by over 95%, and improved the flexural strength regain by approximately 75% after 56 days of wet-dry incubation. The sustained-release mechanism considerably improved the self-healing performance.