Nata de soya is a fermentation product derived from tofu and tempeh waste, known for its strong and stable cellulose structure. This study focuses on characterizing the porosity and permeability of nata de soya porous membranes modified with various raw material compositions. Porosity and permeability were characterized using Scanning Electron Microscopy (SEM) and fluid flow measurements. The results indicate that the composition of tofu and tempeh waste mixture (Composition A) produced membranes with the highest porosity (51%) and permeability (1.70191 × 10−9 m2). Membranes from tofu waste (Composition B) exhibited 47% porosity and permeability of 1.59554 × 10−9 m2, while membranes from tempeh waste (Composition C) showed 43% porosity and permeability of 1.27643 × 10−9 m2. This research demonstrates that variations in raw material composition and modification processes influence membranes’ porosity and permeability characteristics, contributing significantly to the development of biomass-based materials for filtration applications and supporting efforts toward more sustainable management of organic waste.