In order to achieve antibacterial properties in water-based coatings, two types of antibacterial pomelo peel flavonoid microcapsules were added to water-based coatings and decorated on the surface of fiberboard. The surface coatings of the substrates were tested and analyzed. The antibacterial rate of the surface coatings of the two groups of fiberboards gradually increased with the increase in the content of the microcapsules. The color difference of the surface coatings of both groups increased slightly, the glossiness decreased, the gloss loss rate increased greatly, and the reflectivity increased slightly. The adhesion of the surface coatings of the two groups of fiberboards did not change significantly, the roughness gradually increased, the hardness of the melamine-resin-coated pomelo peel flavonoid microcapsules gradually increased, and the impact resistance slightly improved. Compared with the antibacterial results of the coating without substrate at the same content, the antibacterial effect of the fiberboard surface coating was slightly decreased. Overall, the surface coating on the fiberboard with 9.0% chitosan-coated pomelo peel flavonoid microcapsules demonstrated superior performance, superior coating morphology, and enhanced antibacterial properties. The antibacterial rate was 73.7% against Escherichia coli, and the antibacterial rate was 77.4% against Staphylococcus aureus. The color difference was 3.85, the gloss loss rate was 90.0%, and the reflectivity was 20.19%. The hardness was HB, the adhesion was level 1, the impact resistance level was 3, and the roughness was 1.94 μm. This study explored the effect of antibacterial microcapsules on coating performance, providing a technical basis for the application of the antibacterial microcapsules.