The paper presents results of the studies on the removal of protein impurities from the system components of transmission installation in an ultrasonic cleaner. Contamination was removed from the places susceptible to underwashing in Clean In Place systems, from elbows, flap and ball valves and tees. The aim of this study was to evaluate the effectiveness of the cleaning process in an ultrasonic cleaner depending on the power of ultrasound, a chemical (NaOH), temperature, and duration of the process. To evaluate the effectiveness of the method of cleaning Clean-Trace™ Surface Protein Plus visual tests were applied, which were based on the color reaction of copper and the protein complexes in the 5-point scale. Application of ultrasound and clean water does not completely remove protein contaminants from the cleaned surfaces. Application of chemical and high temperature improves the efficiency of the process. The fastest maximum cleaning efficiency was achieved in an ultrasonic cleaner at full load and 40°C of ultrasound.