Abstract This paper proposes two different health-aware economic predictive control strategies that aim at minimizing the damage of components in a pasteurization plant. The damage is assessed with a rainflow-counting algorithm that allows estimating the components’ fatigue. By using the results obtained from this algorithm, a simplified model that characterizes the health of the system is developed and integrated into the predictive controller. The overall control objective is modified by adding an extra criterion that takes into account the accumulated damage. The first strategy is a single-layer predictive controller with an integral action to eliminate the steady-state error that appears when adding the extra criterion. In order to achieve the best minimal accumulated damage and operational costs, the single-layer approach is improved with a multi-layer control scheme, where the solution of the dynamic optimization problem is obtained from the model in two different time scales. Finally, to achieve the advisable trade-off between minimal accumulated damage and operational costs, both control strategies are compared in simulation over a utility-scale pasteurization plant.