In this study, cellulose nanocrystals (CNC) as functional cross-linker and Pickering emulsifier was used to stabilize Lysozyme (Lys) encapsulated in quaternary ammonium chitosan nanoparticles (QC NPs) via ionic gelation method. Physicochemical, structural, and antibacterial properties of the CNC stabilized Lys loaded QC NPs were also evaluated. Particle size, particle size distribution, Zeta potential (ZP), and spectroscopic analyses showed the successful encapsulation of Lys. Antibacterial activity of NPs against Staphylococcus aureus and Vibrio parahaemolyticus was investigated on the basis of inhibition zone (IZ), minimum inhibitory concentration (MIC), and minimum bacterial concentration (MBC). MIC and MBC of CNC stabilized Lys loaded HQC NPs against S. aureus were 0.094 and 0.188 while corresponding values for CNC stabilized Lys loaded LQC NPs V. parahaemolyticus were 0.156 and 0.312 mg/mL, respectively. Therefore, CNC stabilized Lys loaded QC NPs have potential implications in the food industry for food preservation and packaging. •CNC stabilized Lys loaded QC NPs has successfully been prepared using ionic gelation method.•Physicochemical properties CNC stabilized Lys loaded QC NPs were investigated.•Antibacterial activity of CNC stabilized Lys loaded QC NPs was evaluated.•Proposed mechanisms of CNC stabilized Lys loaded QC NPs were tentatively discussed.