The use of nanostructured materials is an intriguing approach for developing composite of enzyme-nanomaterials since these materials can provide a large surface area, which can lead to high volumetric enzyme activity. Recent advances in enzyme aggregation protocols via a cross-linking method are promising for the development of highly stable and active composite of biocatalytic-nanomaterials. Significant enhancement of enzyme stabilization was realized by introducing cross-linked enzyme aggregates (CLEAs) via glutaraldehyde mediated coupling with nanofibers. The enzyme stability of enzyme aggregated nanofibers was greatly enhanced with essentially no measurable loss of activity over a month or several days of observation under rigorous shaking condition. The nanofibers coated with proteases and esterases aggregation, repectively were implemented for application in biodegradation. This approach offers a useful biocatalytic system with potential applications in biosensor, bioelectrochemistry, bioremediation and bioconversion.