The article presents the development of interpenetrating polymer network (IPN) membranes from natural compounds, specifically agarose and natural rubber latex, for sustainable molecular sieving. The membranes were fabricated without using toxic cross-linking agents, addressing the urgent need for sustainable alternatives to fossil-based polymer materials. The biopolymers were self-assembled and self-cross-linked to form patchlike nanodomains, which were characterized using nano-FTIR spectroscopy and computational methods. The resulting membranes exhibited excellent solvent resistance and tunable molecular sieving capabilities, with control over separation performance through adjustments in membrane composition and activation in water. The membranes successfully removed carcinogenic impurities at concentrations below the threshold of toxicological concern, demonstrating their effectiveness in active pharmaceutical ingredient (API) purification. Additionally, the biodegradability of the membranes was assessed, showing their environmental friendliness. The study highlights the potential of IPN membranes derived from natural materials for sustainable and cost-effective membrane fabrication.The article presents the development of interpenetrating polymer network (IPN) membranes from natural compounds, specifically agarose and natural rubber latex, for sustainable molecular sieving. The membranes were fabricated without using toxic cross-linking agents, addressing the urgent need for sustainable alternatives to fossil-based polymer materials. The biopolymers were self-assembled and self-cross-linked to form patchlike nanodomains, which were characterized using nano-FTIR spectroscopy and computational methods. The resulting membranes exhibited excellent solvent resistance and tunable molecular sieving capabilities, with control over separation performance through adjustments in membrane composition and activation in water. The membranes successfully removed carcinogenic impurities at concentrations below the threshold of toxicological concern, demonstrating their effectiveness in active pharmaceutical ingredient (API) purification. Additionally, the biodegradability of the membranes was assessed, showing their environmental friendliness. The study highlights the potential of IPN membranes derived from natural materials for sustainable and cost-effective membrane fabrication.