In the present study, nanofiller (polypyrrole and chitosan (CPY) composite) incorporated polysulfone (PSF) based hollow fiber was synthesized to address the membrane fouling in ultrafiltration of sugarcane juice. The CPY was incorporated within the PSF matrix at varied concentrations (0.25, 0.5 and 1 wt%). The synergy between CPY and PSF was examined by X-ray diffraction and Fourier transform infrared spectroscopy. Morphological results confirmed the augmented porous nature of the modified membrane. The optimized membrane (MHCPY_0.5) displayed improved membrane properties along with the rejection of polyphenoloxidase enzyme (71.2%) and bacteria (5.4 log reduction). The antifouling nature of the selected modified membrane was evaluated in terms of resistances and flux recovery ratio and the same was compared with that of unmodified membrane. The MHCPY_0.5 exhibited remarkable antibacterial properties confirmed from halo zone, shake flask, anti-adhesion, live dead staining assays studies. • Composite HF membrane was tested for anti-fouling and anti-microbial properties. • Membrane permeability was increased 4 times by 0.5% chitosan-polypyrrole composite. • 71% PPO rejection was obtained using the modified membrane. • FRR of the modified membrane was 72% compared to 54% of the unmodified one. • The modified membrane showed remarkable antimicrobial property.