The results of cleaning procedures are sometimes very difficult to determine using only flux recovery data. It is of interest to know in what way the cleaning agent reacts with the membrane and whether it actually modifies the membrane in such a way that fouling is prevented. Zeta potentials of virgin and cleaned membranes have not been measured and compared previously, even though it has been noticed that cleaning often increases the flux of the virgin membrane. As the membranes in industry are always cleaned, it is important to be able to follow the cleaning efficiency after several cleanings to be able to approximate the lifetime of the membrane for a certain process. In this study, the influence of chemical cleaning on the fluxes and charges of ultrafiltration membranes fouled with two different proteins were investigated. Using simultaneous streaming potential and flux measurements, virgin, precleaned, fouled and cleaned membranes were compared. The measured streaming potentials were recalculated to zeta potentials. FTIR spectra were made from one series of experiments. Polysulfone membranes (cut-off, 50 000 g mol −1) and HEKLA membranes (cut-off, 20 000 g mol −1) were cleaned before and after fouling with 80 ppm bovine serum albumin (BSA) at its isoelectric point at pH 5 or with lysozyme (LYS) at pH 5, 6 and 7. Six kinds of chemicals were used as the cleaning agents. The precleaning modified the membranes, but the extent depended on the cleaning agents used. The calculated zeta potentials of the membranes changed after cleaning and, in addition, the flux of the HEKLA membranes increased. Fouling was easier to remove when it was situated only on the surface of the membranes, as with the smaller pore size membranes. The best cleaning results were obtained using sodium hydroxide at high temperature and without pressure. Both acidic and basic cleaning agents could be used to clean the BSA fouled membranes. With FTIR it could be seen that cleaning did not totally remove fouling because some peaks of the clean membrane were missing and others had appeared. The FTIR data seemed to give some hint of what chemical groups in the membrane adsorbed the protein. The charge characterization can be used to determine cleaning efficiency if the zeta potential of the fouled membrane differs from the clean one by at least some millivolts at some characteristic pH. This technique is to be tried out with different combinations of proteins and membranes and for more complicated cleaning sequences.