Since a concrete structure exposed to a sulfate environment is subject to surface ion ingress that yields cracking due to concrete swelling, its service life evaluation with an engineering modeling is very important. In this paper, cementitious repair materials containing bacteria, Rhodobacter capsulatus, and porous spores for immobilization were developed, and the service life of RC (Reinforced Concrete) structures with a developed bacteria-coating was evaluated through deterministic and probabilistic methods. Design parameters such protective coating thickness, diffusion coefficient, surface roughness, and exterior sulfate ion concentration were considered, and the service life was evaluated with the changing mean and coefficient of variation (COV) of each factor. From service life evaluation, more conservative results were evaluated with the probabilistic method than the deterministic method, and as a result of the analysis, coating thickness and surface roughness were derived as key design parameters for ensuring service life. In an environment exposed to an exterior sulfate concentration of 200 ppm, using the deterministic method, the service life was 17.3 years without repair, 19.7 years with normal repair mortar, and 29.6 years with the application of bacteria-coating. Additionally, when the probabilistic method is applied in the same environment, the service life was changed to 9.2–16.0 years, 10.5–18.2 years, and 15.4–27.4 years, respectively, depending on the variation of design parameters. The developed bacteria-coating technique showed a 1.47–1.50 times higher service life than the application of normal repair mortar, and the effect was much improved when it had a low COV of around 0.1.