The enhancement of the cleaning efficiency of cleaning-in-place (CIP) systems is playing a key role in improving food production. Cleaning models based on computational fluid dynamics (CFD) can be a tool that enables identifying locations in a plant that are difficult to clean and enhances the cleaning efficiency by appropriate fluid dynamics, that is, the application of transient flow. A CFD cleaning model was developed that is based on the assumption of a mass transfer controlled cleaning process. The physical basis of the model is the analogy between heat and mass transfer. A validation of the cleaning mechanism, using experimental data of local cleaning times in several complex geometries with varied static and transient flow velocities, was carried out. A modified waxy maize starch with phosphorescent tracers was used as model food soil. The received results show a good agreement between the measured and simulated cleaning times. The cleaning model is suitable for the calculation of the cleaning progress for all fouling systems, where the cleaning mechanism is mass transfer controlled. It is now possible to visualize the effect of complex pipe geometries or inappropriate hygienic design on the overall cleaning time. Especially in locations difficult to reach with steady flow, the application of pulsed flow shows a shorter cleaning time. Based on the presented new CFD model the local cleaning efficiency can be predicted.