It is of significant interest to create functional flexible surfaces that simultaneously exhibit high water-resistance and antimicrobial performances for medical or packaging applications. This study reported a synthesis of functional surface coating on flexible cellulose materials (filter papers) with ZnO nanoparticles and binds of renewable soybean oil-based polymers. Self-aggregation of ZnO nanoparticles could form ZnO particles with two regular morphological patterns. Rather than a rod-like morphology, a flower-like ZnO benefited a promotion of surface hydrophobicity. Moreover, surface with the flower-like ZnO showed a 51.6% promotion on antimicrobial activities against Gram-negative bacteria (E. coli) than the rod-like ZnO. A low binder/ZnO ratio of 0.2 led to a remarkable improvement on water repelling performances without negative effects on a coating adhesion of ZnO. Under this condition, a hydrophobic surface was achieved with a large static contact angle of 138° when applying ZnO nanoparticles at a dosage of 3 g m−2.