A computational fluid dynamics model was designed to study the problem of thermal processing of a liquid food product containing whey proteins within a heat exchanger consisting of heating, holding and cooling tubular sections. This physical problem is associated with strong coupling between the phenomena of fluid flow, heat transfer, and thermal denaturation-aggregation of whey proteins. Our primary objective was to investigate the two-way coupling between these phenomena within the heat exchanger. This was carried out by analyzing the model predictions of velocity, temperature and product properties at both axial and radial directions. Attention was focussed on the whey proteins present in a cream cheese formulation. The thermal denaturation-aggregation kinetics was supposed to follow that of the beta-lacto-globulin, which plays a major role in fouling when milk derivatives are submitted to thermal processing in heat exchangers. Model predictions demonstrated that the apparent viscosity of the liquid product exhibited a complex behavior along the processing unit: in addition to its dependence on local temperature, it was affected by the local degree of denaturation of whey proteins – and hence on the product history previous to this position in the heat exchanger. The numerical model was structured into a sequence of computational domains; its versatility was illustrated by changing the length of the holding section and then assessing the impact on the final degree of denaturation of the whey proteins present in the liquid product.