Selenium nanoparticles (Se(0)NPs) have been well-characterized; however, whether processing affects their physicochemical and functional properties remains unknown. Here, chitosan (low and high molecular weight; CS(L) and CS(H), respectively) was used to stabilize Se(0)NPs, and the effects of heating (37 degrees C, 70 degrees C, and 95 degrees C), freeze-drying-rehydration, and freeze-thawing on CS-Se(0)NPs physicochemical stability, Se release, antioxidant capacity, and antibacterial activity were evaluated. The results demonstrated that all treatments could cause CSSe(0)NPs aggregation and Se release to varying degrees. Aggregation of CS-Se(0)NPs decreased their antibacterial activity, while Se release increased their antioxidant capacity with negligible effects on antibacterial activities. None of the CS-Se(0)NPs could tolerate freeze-thawing. CS(H)-Se(0)NPs exhibited better rehydration and heating stability than CS(L)-Se(0)NPs, although "rod-like" triclinic crystalline Se in CS(H)-Se(0)NPs, produced by 95 degrees C heating, decreased both antioxidant and antibacterial activities. Thus, these results provide a theoretical basis for the development and suitable application of CS-Se(0)NPs.