Fibrous membranes based on polyhydroxybutyrate/poly-ε-caprolactone (PHB/PCL) blends were obtained by electrospinning. Composite nanoparticles produced from N-halamine precursors and silane precursors were used to modify silica hydrosol which were obtained by the condensation of tetraethylorthosilicate followed the Stober method. The produced composite nanoparticles were characterized by TEM and FT-IR. The dip-pad process was used to coat the synthesized silica composite nanoparticles onto the fibrous membrane. The coated PHB/PCL fibrous membranes were characterized by SEM, FT-IR and TGA. After chlorination, the chlorinated fibrous membranes showed excellent hydrophobicity with water contact angle of 151 ° ± 1° and exhibited effective antimicrobial activity against Escherichia coli O157:H7 and Staphylococcus aureus with 99.95% and 99.91% bacterial reduction within 60 min of contact time, respectively. The coated membranes showed good stability and durability toward UVA light exposure and storage. The cell biocompatibility test indicated that the membranes have no cytotoxicity. Therefore, the designed antibacterial fibrous membranes with super hydrophobicity may have great potential for use in food packaging and biomedical materials.