The use of microdevices in extraction processes in aqueous two-phase systems (ATPS) has been studied for years in the literature. However, the effects of flow patterns still need to be adequately explored, especially for real samples. In this sense, the present study investigated the performance of microdevices in the recovery and partial purification of invertases with varying flow patterns. The invertases from Saccharomyces cerevisiae and the polyethylene glycol 1500/magnesium sulfate system were used in the experiments. Beyond the flow pattern, the study sought to maximize recovery and purification factor (PF) values by varying other operating conditions, including residence time, volumetric ratio, and channel diameter. It was observed that the short slug and long slug patterns showed better separation performance than the parallel pattern regardless of residence time and volumetric ratio. Increasing the residence time from 15 to 35 min increased the top recovery and PF values by two times, indicating that S. cerevisiae invertase partition is slow to the top phase. The maximum values of recovery (57.01 % ± 2.67 %) and PF (4.16 ± 0.06) were reached in the condition with long slug pattern, 35 min of operation, volumetric ratio of 2:1, and a channel diameter of 0.51 mm. The present study provides valuable information for integrating microdevices in a protocol for purifying invertase from S. cerevisiae and other proteins in real systems.