Pomelo peel is a natural substance with antibacterial properties. Its extraction process is simple, and the raw materials are abundant. Microcapsules were prepared using melamine resin as the wall material and pomelo peel flavonoids as the core material. The optimization of microcapsule preparation was explored by orthogonal and single-factor experiments. The findings indicated that the optimum process for the preparation of microencapsulation was a 0.12:1 mass ratio of core to wall material, 60 °C microencapsulation reaction temperature, 800 rpm microencapsulation reaction stirring speed, and 2% emulsifier concentration. On this basis, the microcapsules were applied to waterborne coatings at different levels, 0%, 3.0%, 6.0%, 9.0%, 12.0%, and 15.0%, respectively, to prepare paint films, and the properties of the paint films were tested and explored. The test showed that the microcapsules added to the waterborne paint film exhibited antibacterial activity while retaining good optical and mechanical properties. In comparison with Escherichia coli, the microcapsules had a greater antibacterial rate against Staphylococcus aureus. When the content of microcapsules was 6.0%, the general performance of the waterborne paint film was optimal. The antibacterial rate of the paint film against Staphylococcus aureus and Escherichia coli was 40.5% and 50.5%, respectively. The color difference was 3.28. The paint film had a certain elasticity area, the elongation at break was 10.8%, and the roughness was 1.75 μm. We successfully prepared microcapsules capable of improving the antibacterial performance of waterborne paint film, which expands the application field of waterborne coatings and provides a certain reference value for the antibacterial research of waterborne coatings.