Cellulase containing nanobiocatalysts have been useful as an extraction tool based on their ability to disrupt plant cell walls. In this work, we investigate the effect of nanoparticle composition and chemical linkage towards immobilized cellulase activity. Cellulase nanoconstructs have been prepared, characterized and compared for their loading efficiencies with standard assays and enzyme kinetics and correlate well with the cognate loading efficiencies. Application of the cellulase-immobilized nanoparticles on onion skins results in release of a distinctive composition of polyphenols. The aglycosidic form of quercetin is the dominant product of onion skin hydrolysis affected by cellulase nanobiocatalysts. Chitosan-coated iron oxide nanoparticles with APTES-conjugated cellulase are found to be most effective for polyphenol release and for transformation of glycosidic to aglycosidic form of quercetin. These results shed light on the activity of immobilized cellulase beyond their role in cell wall disruption and are important for the practical application of cellulase nanobiocatalysts.