This study tested, for the first time, electromembrane extraction (EME) as a fast, high-throughput (96-well) way to remove unconjugated fluorescein isothiocyanate (FITC) from fluorescently labeled protein samples, achieving >90% dye clearance while retaining the labeled protein. Flow Induced Dispersion Analysis (FIDA) was then used to confirm the human serum albumin/FITC complex remained functional after purification, measuring its binding to an anti-HSA antibody (Kd 0.8 µM, hydrodynamic radius 5.87 nm), consistent with prior values. It is an example of using FIDA to confirm binding affinity and size of a labeled protein in solution.