An enhanced water flux and anti-fouling nanocomposite ultrafiltration membrane based on quaternary ammoniumpropylated polysilsesquioxane (QAPS)/cellulose acetate (QAPS@CA) was fabricated by in situ sol-gel processing via phase inversion followed by quaternization with methyl iodide (CH3I). Membrane characterizations were performed based on the contact angle, FTIR, SEM and TGA properties. Membrane separation performance was assessed in terms of pure water flux, rejection and fouling resistance. The 7%QAPS@CA nanocomposite membrane showed an increased wettability (46.6° water contact angle), water uptake (113%) and a high pure water permeability of ∼370 L m−2 h−1 bar−1. Furthermore, the 7%QAPS@CA nanocomposite membrane exhibited excellent bactericidal properties (∼97.5% growth inhibition) against Escherichia coli (E. coli) compared to the bare CA membrane (0% growth inhibition). The 7%QAPS@CA nanocomposite membrane can be recommended for water treatment and biomedical applications.