Two types of microcapsules were added to the coating separately. The specifications of the poplar board were 50 mm × 50 mm × 8 mm. The antibacterial rate of the poplar board surface gradually increased with the increase in the microcapsule content, and the antibacterial activity for Staphylococcus aureus was slightly higher than that against Escherichia coli. Influenced by the change in the wood grain’s color on the poplar board itself, both microcapsules had no significant effect on the chromaticity value and color difference of the poplar board surface, as well as the reflectance of the visible light band. The glossiness decreased with the increase in the microcapsule content, and the gloss loss rate increased with the increase in the microcapsule content. With the increase in the microcapsule content, the hardness of the poplar board surface in both groups increased slightly, and the roughness increased gradually. The adhesion of the poplar board surface coating with melamine-resin-coated pomelo peel flavonoid microcapsules was slightly reduced, and the impact resistance was not significantly affected. Chitosan-coated pomelo peel flavonoid microcapsules had no significant effect on the adhesion of the poplar board surface coating, and the impact resistance increased slightly when the content of microcapsules was higher. Comprehensively, the poplar board coating with 9.0% chitosan-coated pomelo peel flavonoid microcapsules had a better overall performance, with antibacterial activities for Escherichia coli and Staphylococcus aureus of 70.6% and 77.6%, respectively. The color difference was 6.70, the gloss loss rate was 53.9%, the reflectivity was 50.60%, the hardness was H, the adhesion was grade 1, the impact resistance was grade 2, and the roughness was 2.10 μm. The results provide technical references for the application of antibacterial microcapsules of pomelo peel flavonoids on the surface of wood materials.