In this paper, the mineralization effects of ureolytic type microorganism were employed in the surface treatment of concrete after carbonation. The capillary water absorption, resistance to water permeation, and rapid chloride permeation (RCP) of concrete were tested after treatment. The contact angle of the surfaces was measured. The morphology and composition of the deposits were comprehensively studied. The results show that both carbonation and microbial surface treatment can increase the resistance to permeability while reducing the water absorption of concrete. Large calcite crystals, which tightly adhered to the concrete surfaces, are formed by microbial treatment. Carbonation has no impact on the crystalline and morphology of microbial precipitates. However, after microbial surface treatment, different effects are observed on the water absorption and permeation of concrete with or without carbonation. When microbial surface treatment is performed after carbonation, the range of further reduction in terms of water absorption coefficient is higher compared with the reduction by the treatment on uncarbonated concrete. The main reason for this phenomenon is that the degree of hydrophilicity of concrete after carbonation decreases after microbial surface treatment.