Through a study of the effect of hydrodynamics on the cleanability of complex equipment, this work demonstrates the need for hygienic design to significantly improve food safety. A three-way valve was contaminated with Bacillus spores, isolated from a dairy production line and then suspended in custard. The valve was cleaned by a CTP procedure, including both alkaline and acid phases. The residual localized contamination was assessed directly on the internal surfaces in contact with the food product. Wall shear stress was measured in selected zones by an electrochemical method. Rubber materials (seat areas) are usually considered to be poorly cleanable, yet were found to be more cleanable than adjacent stainless steel zones. This observation emphasizes the importance of the geometry on the cleanability level, and the flow pattern during the cleaning process. Despite its low level, the contribution of the mean wall shear stress, together with its fluctuation rate, was demonstrated in a complex piece of equipment. This underlines the importance of the flow pattern in machinery and more generally in production systems which are automatically cleaned in place. In the upper part of the valve, cleanability was ensured by higher values of local mean wall shear stress, while near its outlet the same cleanability was obtained due to a wide variation in wall shear rates.