Since many industrial processes are not operated continuously, large shares of the heat recovery potential in those processes can only be achieved indirectly. While conceptual design methods to integrate stratified thermal energy storage systems are being developed, the control of the resulting systems is addressed in this paper. The main challenge of the control of heat exchangers in stratified storage systems is the fact that both outlet temperatures of the heat exchanger need to be maintained at their setpoint. A simulation model describing plate heat exchangers and based on this a control strategy are presented. The simulation model is experimentally validated and represents the real heat exchanger with a steady state error within the bounds of ± 0.31 K. The control strategy contains a feed forward path using measured disturbances and a lookup table to set the intermediate loop-sided mass flow rate. Furthermore, one feedback PI controller is used to control one outlet temperature by adjusting the intermediate loop-sided inlet temperature with a mixing valve. As the lookup table is based on a sufficiently accurate description of the heat exchanger characteristics, the second outlet temperature (process-side) is maintained within bounds of ± 0.5 K. For further development, the measurement effort is recommended to be reduced by means of state and disturbance estimation. The rather rigid control algorithm might be replaced with a multivariable control approach such as model predictive control in order to increase the versatility of the system.