This study presents a time-efficient, two-step modification strategy to significantly enhance polybenzimidazole (PBI) membrane resistance to acids and organic solvents, targeting low-pH aqueous and organic solvent nanofiltration (OSN) for industrial applications. A green solvent-based aqueous Fenton reaction pretreats the membrane, improving chemical and thermal stability via enhanced chain interactions. Subsequent Thiol-Ene click chemistry crosslinking introduces crucial flexibility, compensating for Fenton-induced brittleness. This synergistic PBI-FT membrane demonstrates remarkable stability in 70 % HNO3 (maintaining > 80 % MgSO4 rejection) and highly polar aprotic solvents (DMAc, DMF, NMP), retaining > 97 % weight. In OSN, PBI-FT achieved 2.1 LMH/bar ethanol permeance with > 97 % Rose Bengal rejection, showing superior separation even after 168 h DMF exposure. This sustainable technique yields robust nanofiltration membranes for efficient separation processes in challenging industrial environments.