Due to the widespread application of plate heat exchangers (PHE) in the food industry, a key aspect of their operation is ensuring a high level of hygiene, which guarantees the microbiological cleanliness of the final product. This is achieved through the cleaning of installations containing PHE using the Clean-in-Place (CIP) system. An important aspect is the determination of flow resistance, as this enables the specification of drive parameters and the selection of a pump that provides a sufficiently high flow rate through the installation, particularly required during the pre-rinsing stage. The subject of the research was a three-section plate heat exchanger, which forms part of a prototype technological line designed for the pasteurisation of liquid egg mass and its fractions – egg white and yolk. As part of the study, the effectiveness of the cleaning process was assessed depending on the flow rate. Based on experimental results, the minimum flow rate necessary for effective cleaning using commercial sodium hydroxide (NaOH)-based cleaning agents was determined. In addition, the extent to which the relationship described in the literature – linking flow rate with hydraulic resistance in PHE – is confirmed under real operating conditions during the cleaning process in the CIP system was analysed. The results obtained may be used to optimise the parameters of the CIP process, which will contribute to increased efficiency, reduced consumption of chemical agents, and improved microbiological safety of the final product.