The temperature of the feed is known to be an important factor affecting the formation and the growth rates of bacterial communities on dairy filtration membranes. However, decades after the integration of filtration processes in the dairy industry, there is still questioning whether filtration should be performed at cold (<15 degrees C) or hot (>48 degrees C) temperature. A biofilm reactor designed to mimic a filtration system was used to provide answers to this question. Bacteria adhering and growing on ultrafiltration membranes in contact with pasteurised skim milk were characterised at 15 degrees C and 50 degrees C through a metabarcoding approach. Our results suggested that the processing time should be limited to 10 h at 50 degrees C to avoid the exponential growth of thermophilic spore-former bacteria, while the use of 15 degrees C combined with daily cleaning procedures appeared the best way to retard the formation of biofilms on membranes.