We report on the effect of electrode geometry on alternating current cloud point extraction (ACPE). ACPE is a technique utilized to extract membrane-associated biomolecules in an electrode-integrated microfluidic channel. In this study, we investigated the effect of gap size (4 approximate to 22 m) between microband electrodes on ACPE. A decrease in gap size resulted in efficient and rapid concentration of fluorescent-labeled phospholipids, a model of membrane-associated biomolecules. We also investigated the effect of applied voltage amplitude on ACPE using devices with decreased electrode gap size. When the gap was small, ACPE was achieved with low applied voltages. ACPE of membrane proteins extracted from HeLa cells was also studied to demonstrate the applicability of the ACPE to real samples. The results provide a guideline to improve the performance of ACPE and facilitate application of the ACPE technique as part of an overall analytical process.