Phenylalanine dehydrogenase (PheDH; EC 188.8.131.52) is an important enzyme of amino acid dehydrogenases family that increasingly used as a valuable biocatalyst in neonatal screening kits and synthesis of L-phenylalanine. The goal of this literature was to find a suitable purification method for recombinant Bacillus badius PheDH by practical comparison between chromatographic and polyvinyl pyrrolidone (PVP)/Na2SO4 aqueous two-phase systems (ATPS) techniques. The partitioning behavior of target enzyme in PVP/Na2SO4 ATPS was examined and compared with the obtained results from a chromatographic protocol. Direct comparison of chromatography and ATPS procedures clearly revealed that the ATPS consisting of 8.0% (w/w) PVP, 17.0% (w/w) Na2SO4 with pH of 8.0, VR=0.25 and temperature of 25 °C was the most desirable process for PheDH purification. A specific activity of 1231.42 U/mg, a purification factor of 36.61, a yield of 95.5% and a recovery of 138.9% were achieved. Altogether, we presented a two-phase methodology as a scalable and economically alternative for the production of PheDH enzyme.