Fluoroalkyl end-capped N-(1,1-dimethyl-3-oxobutyl)acrylamide oligomer [R-F-(DOBAA) (n)-R-F] reacted with tetraethoxysilane (TEOS) and silica nanoparticles in the presence of low-molecular weight biocides such as hibitane, hinokitiol, and hinokioil under alkaline conditions to afford R-F-(DOBAA) (n)-R-F/silica nanocomposites-encapsulated these biocides in excellent to moderate isolated yields. Fluoroalkyl end-capped N,N-dimethylacrylamide oligomer [R-F-(DMAA) (n)-R-F] and acrylic acid oligomer [R-F-(ACA) (n)-R-F]/silica nanocomposites-encapsulated hibitane were obtained under similar conditions. Dynamic light scattering measurements showed that the size of these fluorinated nanocomposites-encapsulated biocides thus obtained is nanometer size-controlled. Additionally, these fluorinated nanocomposites were shown to have a good dispersibility and stability in methanol and water. Of particular interest, these fluorinated nanocomposites-encapsulated biocides were found to have a good antibacterial activity against Staphylococcus aureus, and these nanocomposites were applied to the surface modification of traditional organic polymers such as poly(methyl methacrylate).