The partition of glutamate decarboxylase (GAD) from Escherichia coli in polyethylene glycol (PEG) and sodium sulfate aqueous two-phase systems (ATPS) has been explored with the purpose of establishing a phase system for the purification of GAD after cell disruption. The results showed that the partitioning of GAD was slightly influenced by PEG molecular weight (MW) but depended on the tie line length (TLL) and NaCl and loading sample concentrations. The optimum system obtained for GAD purification was composed of a PEG MW of 4,000, TLL of 63.5%, a volume ratio of 2.31, a loading sample concentration of 0.4 g/mL, which produced a GAD recovery of 90% with the purification fold of 73. Furthermore, the feasibility of directly purifying GAD from the cell disrupts using ATPS was evaluated. The established ATPS for GAD purification exhibited an efficient integrated purification process compared to the reported purification process in terms of purification efficiency and recovery.