The amount of free glycerol in the final product of biodiesel is limited by international standards. In the current study, optimized solvent-resistant nanocomposite membranes were prepared using the phase inversion method based on a poly(ether sulfone) (PES) membrane modified by adding different concentrations of functionalized multiwall carbon nanotubes (MWCNTs-NH2). The FUR results confirmed the occurrence of modification on neat MWCNTs. The characteristics and properties of the mixed matrix membranes were analyzed by using SEM and AFM as well as contact angle measurements and molecular weight cutoff (MWCO), and pore size properties were also studied. Contact angle results indicated that the surface hydrophilicity was improved by increasing MWCNTs content. Unmodified PES and PES/MWCNTs-NH2 mixed matrix membranes were evaluated in terms of the flux behavior of pure water and other polar and nonpolar solvents, surface roughness, swelling, and antifouling performances as well as their ability to remove free glycerol from biodiesel-rich phase. The % FRR of the modified membranes increased from 22.36% for M-0 to 59.49% for M-2, while increasing the MWCNTs-NH2 amount from 0.00 to 0.05 wt % led to a decrease of R-ir from 77.63% to 40.50%. Furthermore, the 0.05% w/w MWCNTs-NH2 modified membrane showed promising capability in removing about 99.5% of free glycerol with superior reusability, while no significant change happened in biodiesel rejection.