In this study, a new class of heterogeneous membranes based on cellulose acetate (CA) polymer and a complex filler clay‐silica nanowires (SiO2NWs) was investigated for potential biomedical applications. SiO2NWs were synthesized using natural clay through a facile sol–gel method and were dispersed in the polymer solution by sonication in the 1.25, 2.5, and 5% weight ratio to the CA acetate polymer. Membranes were subsequently prepared via phase inversion by precipitation of the CA polymer in water. The pristine CA membrane and SiO2NWs based nanocomposites membranes were characterized using different characterization techniques. The presence of the SiO2NWs in the CA membrane was found to significantly enhance the protein retention, water wettability and thermal as well as mechanical properties in comparison to the pristine CA membrane. Water flows studies at different temperatures and the retention of bovine serum albumin have been studied and the nanocomposite membranes were found to exhibit superior performances compared with the pristine CA membranes. SiO2NWs‐CA membranes showed a much higher stability to the water temperature change during separation than CA membranes. Morphological changes clearly revealed that the composite membrane were much more compact than the pristine CA membranes. The rabbit dermal fibroblasts cell viability in cultures after 72 hr of incubation was found to be greater than 80%. These newly synthesized composite membranes exhibit a high potential to be used for various medical applications because of their non‐cytotoxic characteristics. Copyright © 2016 John Wiley & Sons, Ltd.