Membranes that can separate small molecules and ions are of immense interest in various separations. Self‐assembling zwitterionic amphiphilic copolymers (ZACs) are extremely promising as exceptionally fouling‐resistant membrane selective layers with narrow size cut‐offs. However, it is difficult to tune their effective pore size within time frames compatible with roll‐to‐roll manufacturing. We report a novel, ultra‐fast approach for tuning the pore size of ZAC‐based membranes through thiol‐ene click chemistry that brings the needed post‐modification time from tens of minutes to only 10–40 s, making its integration feasible in large scale manufacturing systems. Resultant membranes have enhanced organic molecule and salt rejections, resulting in tunable mono‐/divalent ion selectivity. For instance, cross‐linking increases Na2SO4 rejections from <20% to up to 83%, while NaCl rejection remains below 30%. Furthermore, these membranes completely resist fouling by oil and proteins, outperforming commercial membranes. These results suggest that our cross‐linked membranes have the potential to be used in separations in the food industry, pharmaceutical manufacturing, and wastewater treatment.