In the literature, it has been observed that in the cleaning of whey-fouled membranes, the flux recovery can decrease dramatically when using high pH and temperature when the permeate side is kept open. The only hypothesis presented so far states that the in-pore deposits swell in contact with aqueous NaOH, narrowing the membrane pores and hence, reducing the filtration flux. This hypothesis does not explain why the swollen deposits are not dissolved at high pH. In this paper, it is proposed that whey deposits are transformed into gels resulting from contacting NaOH. The gelling process increases significantly the resistance of the deposits to alkali. The kinetics of the caustic-induced gelation of whey protein concentrate solutions was found to verify that this gelling process could occur in similar conditions of pH and temperature as those used in the cleaning operations. The formation of a gel layer in a whey solution in contact with an alkaline solution was also investigated.