In this research, the preparation and characterization of naringinase nanobiocatalyst that was comprising of nano-magnetic cross-linked enzyme aggregates of naringinase (NM-NGase-CLEAs), which was covalently bounded to lysine-assisted magnetic nanoparticles, were studied. Among the six different precipitants, tert-butanol performed the best for naringin hydrolysis. The optimal conditions for the immobilization process required 10 mM glutaraldehyde, 1:10 ratio of lysine/enzyme, and 3 h crosslinking at 3–4ºC. The morphology of the NM-NGase-CLEAs implied a non-uniform, semi-pyramid and semi-cubic rods. The dynamic light scattering (DLS) results showed that the nanomagnetite particle size was around 81.9–96.5 nm, with a polydispersity index (PDI) of 0.238 that after immobilization  the particle size was reduced to around 13.2–15.3 nm, with PDI of 0.177, and the Ȥ-potential of -28 mV respectively. Study on thermostability of immobilized naringinase at 40–80ºC revealed that, enzyme half-life (t_1/2) of NM-NGase-CLEAs is increased about 3 folds at 80ºC compared to free one. The thermodynamics study indicated that E_a(in) of the free enzyme increased from 38.51 to 49.14 (KJ.mol^-1) and ΔH* increased from 35.57 to 46.20 (KJ.mol^-1) after immobilization. The K_m values of immobilized enzyme was reduced about 10.7 folds compared to the free enzyme while, the catalytic efficiency (k_cat/K_m) was raised about 10.5 folds after immobilization. The NM-NGase-CLEAs kept 73% of its original activity after 10 cycles. Accordingly, the developed method for nanomagnetic CLEAs preparation has provided an efficient and simple approach with reusability of the enzyme together with ease in enzyme handling.