Manufacturers of polymeric membrane filters used for treating food streams routinely recommend that they are chemically cleaned prior to first use. In this paper, two pre-treatment methods are compared for the filtration of a spent sulphite liquor [SSL] (17.8 wt.% dry solids) using a 20 kg mol−1 molar mass cut off (MMCO) fluoropolymer membrane. In an extension of previous work that considered the effect of the application of a pre-treatment protocol over a single operational cycle, this paper reports the effect of pre-treatment protocols over four complete fouling and cleaning cycles. The pre-treatment methods evaluated were the conditioning with water at 60°C only [Protocol 1], and the conditioning with water at 60°C followed by cleaning with 0.5 wt.% NaOH [Protocol 2]. Results are presented that demonstrate that for the system examined, the positive effect of the NaOH pre-treatment protocol diminished after three complete operational cycles, and disappeared after four cycles.