Composite nanofiltration membranes offer advantages because of synergetic effects among the constituent materials’ properties. However, the sustainability of both the membrane fabrication and the raw materials has been a drawback of this energy-efficient separation technology. We report the facile fabrication of a nanocomposite membrane composed of a two-dimensional (2D) material of reduced graphene oxide (rGO) combined with a one-dimensional (1D) material of a ternary metal-based chalcogenide (NaFeS2 or NFS), using silkworm pupae protein as a natural binder. All the source materials can be derived from either nature or waste, ensuring the sustainability of the membrane and its production method. The structural characteristics of the synthesized membranes were analyzed, and the morphology of the composite membranes was studied thoroughly. Thermogravimetric analysis, differential scanning calorimetry, and nanoindentation characterizations indicated that the composite membranes were mechanically and thermally stable. The water and acetone fluxes; salt, dye, and pollutant rejections; and long-term membrane performance were evaluated using a cross-flow filtration system. Solute rejection was observed to increase (up to 98%, 94%, 95%, and 78% for Rhodamine B, 2,4-dichlorophenol, MgCl2, and NaCl, respectively) with increasing concentration of the nanomaterials in the membrane. The fine-tuning of the molecular weight cut-off from 794 to 600 g mol–1 was achieved by varying the concentration of the nanomaterials from 1 to 3 mg mL–1 . Our research findings demonstrate the synergetic effects of combining 1D and 2D materials using silkworm pupae binder. The composite membrane was stable in different classes of organic solvents, including hydrocarbons, alcohols, esters, ethers, polar aprotic solvents, halogenated solvents, and ketones. This first use of natural pupae binder in constructing membrane materials paves the way toward the development of more sustainable membranes.