The isolation of beta-nicotinamide adenine dinucleotide is of great importance since it is widely used in different scientific and technologic fields such as biofuel cells, sensor technology, and hydrogen production. In order to isolate beta-nicotinamide adenine dinucleotide, first 3-aminophenyboronic acid functionalized magnetic nanoparticles were prepared to serve as a magnetic solid support and subsequently they were used for reversible adsorption/desorption of beta-nicotinamide adenine dinucleotide in a batch fashion. The loading capacity of the 3-aminophenyboronic acid functionalized nanoparticles for beta-nicotinamide adenine dinucleotide adsorption was 13.0 mu mol/g. Adsorption kinetic and isotherm studies showed that the adsorption process followed a pseudo-second-order kinetic model and the experimental data can be represented using Langmuir isotherm model. The 3-aminophenyboronic acid functionalized magnetic nanoparticles were proposed as an alternative support for the beta-nicotinamide adenine dinucleotide purification. The results elucidated the significance of magnetic separation as a fast, relatively simple, and low-cost technique. Furthermore, the magnetic supports can be reused at least five times for purification processes.