ABSTRACT Imprinted proteins (IPs) are promising alternatives to natural recognition systems, such as biological receptors or antibodies. One of the crucial stages during development of IPs is removal of the template molecules from its complex with the protein. In this study, bovine serum albumin was imprinted in the presence of 4‐hydroxycoumarin (4‐HC); purification of IPs were carried out by dialysis, and fluorescence 3D spectroscopy was used to monitor the IP purification process. Excitation–emission matrix (EEM) was further investigated via several chemometric algorithms (principal component analysis [PCA], parallel factor analysis [PARAFAC], and independent components analysis [ICA]). We found that the models using PARAFAC and ICA worked better than those of PCA. It was shown that PARAFAC and ICA analyses allow not only to recognize IP sample with signal close to nonimprinted protein, but also to provide recommendations on the optimal dialysis time.