A practical procedure for extracting cellulose whiskers (CWs) from ordinary filter paper by acid hydrolysis has been developed. The extracted CWs alone and in combination with nanoclay were used as reinforcing agents for the preparation of green nanocomposites based on jute fabric and glutaraldehyde (GA) cross-linked soy flour (SF). A solution-induced intercalation method was implemented for the successful fabrication of the nanocomposites. The formation of nanocomposites was confirmed by various physicochemical and spectroscopic techniques and by DFT calculations. The results of the various analyses suggest a strong interfacial interaction between the filler and the matrix. The properties of nanopartide-filled SF/jute nanocomposites were compared with those of unfilled composites. Furthermore, the mechanical strength, thermal stability, flame retardancy, and dimensional stability of the filled composites were found to be much better than those of the unfilled composites, allowing the processing of high-performance green nanocomposites.