Commercial grade sulfonated-Polyethersulfone (S-PES) and functionalized multiwall carbon nanotube (f-MWCNT)/polyvinylpyrrolidone (PVP) nanocomposites (NCs) were used to enhance and optimize the antifouling, protein resistance and protein separation properties of the S-PES ultrafiltration membranes. The polarities of sulfonic groups of S-PES, carbonyl carbon of pyrrolidone, hydroxyl and carboxyl groups of f-MWCNT in the membrane composition helped to strongly bind each other through hydrogen bonding, as shown by Fourier-transform infrared spectroscopy (FTIR). These binding forces greatly reduced the leaching of NCs and developed long finger-like projection, as confirmed by elution ratio and cross-sectional studies of the membranes via field emission scanning electron microscope (FESEM). The contact angle was reduced up to 48% more than pristine PES. Atomic force microscopy (AFM) was employed to study the various parameters of surface roughness with 3d diagrams, while grain analysis of membrane surface provided a quantitative estimation about volume, area, perimeter, length, radius and diameter. The NCs/S-PES enhanced the flux rate with an impressive (80–84%) flux recovery ratio and (58–62%) reversible resistance (Rr) value in situ, with 60% and 54.4% lesser dynamic and static protein adsorption. The best performing membrane were reported to remove 31.8%, 66.3%, 83.6% and 99.9% for lysozyme-(14.6 kDa), trypsin-(20 kDa), pepsin-(34.6 kDa) and bovine serum albumin (BSA-66 kDa), respectively.