Expanded polystyrene (EPS) is a low-density material prone to float during composite mixing and vibration. Inspired by this, a two-bacteria-capsule system was reported in this study to enhance the self-healing capacity of cracked mortar. Specifically, the BC-A capsule, containing aerobic bacteria, EPS, and superabsorbent polymer (SAP), and the BC-N capsule, containing anaerobic bacteria and SAP, are prepared through granulation using polyethylene glycol. Sulphoaluminate cement and epoxy resin are used to encapsulate the core materials. The BC-A capsules automatically float in the composite preparation process, while the BC-N capsules are distributed in the middle and bottom regions due to extrusion effect. Upon capsule rupture, the two types of bacteria are released in regions favorable for biomineralization, corresponding to the principle that oxygen concentration reduces along the crack depth. The self-healing behaviour was evaluated as well as the healing products were characterized. The results showed that the capsules cracked simultaneously with the composite and the coating effectively avoided premature release of the self-healing materials. Cementitious composites containing double capsules achieved 90 % closure of cracks with initial widths of 50–600 μm. The three-dimensional healing capacity was significantly enhanced, particularly in terms of impermeability and strength recovery ratio. The main healing products in the cracks were calcite and swollen SAP. The swollen SAP provided nucleation sites and enough water for biomineralization in the healing process.