A rigid mineral-based deposit, termed ultra-high temperature (UHT) fouling, is formed on heat exchanger surfaces during milk processing at 140 °C. The removal of this type of fouling is for the first time assessed using a laser triangulation sensor and a camera, to measure changes in the thickness and to visualize structural changes in the fouling in situ. The process was monitored during both the alkali and acid cleaning steps. There was no global swelling of the fouling layer during alkali cleaning under the investigated conditions. However, significant degradation of the protein network was observed, which affected the acid cleaning step and the efficiency of the cleaning process. We conclude that treatment with alkali is required to facilitate the removal of deposits with high mineral content during the acid cleaning step. The results have implications for optimizing the cleaning process so as to minimize energy expenditure, while ensuring efficient heat transfer and maintaining product quality.