Chemical amination of the enzyme was demonstrated to favor immobilization onto polydopamine (PDA)-coated magnetic nanoparticles (MNPs) for the first time, to the best of the author’s knowledge. MNPs prepared via hydrothermal synthesis were coated with PDA for the immobilization of naringinase. X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, and Fourier-transform infrared spectroscopy showed that the MNPs were composed mainly of Fe₃O₄ with an average size of 38.9 nm, and coated with a 15.1 nm PDA layer. Although the specific activities of α-L-rhamnosidase (RAM) and β-D-glucosidase (GLU) of free naringinase decreased with amination, the immobilization yields of the aminated enzyme increased by more than 40% for RAM and more than 10-fold for GLU. The immobilization improved the enzyme’s thermal stability (at 50 °C), reaching a half-life of 40.7 and 23.1 h for RAM and GLU activities, respectively. The biocatalyst was successfully used for the debittering of grapefruit juice, detecting a reduction in naringin of 56% after 24 h. These results demonstrate that the enzyme amination is an effective strategy to enhance the immobilization on a PDA coating and could be applied to other enzymes in order to obtain an easily recoverable biocatalyst using a simple immobilization methodology.