Fouling is one of the main causes of industrial problems regarding operation and control of shell and tube heat exchangers. Although fouling is a time dependent phenomenon, most papers in the literature focus on fouling mitigation in steady-state heat recovery. In this work, a lumped parameter model to describe timevarying conditions and their influence in controller tuning is presented. For each modeling cell, there are four input variables (inlet temperatures and flow rates for shell and tube sides), which generate two output signals (outlet temperatures for shell and tubes). The influence of fouling in process control is evaluated by considering intermediate values of thermal resistance of fouling (R-f), simulating its variation with time. The model was implemented in MATLAB/Simulink, and simulations have been carried out for different periods of operation. A step change was applied in the shell flow rate to evaluate the response in the tube outlet temperature. Results show that periodic fitting in proportional integral derivative (PID) parameters are needed to keep the tube outlet stream at the desired temperature. Moreover, two optimization strategies are presented for tuning controller gains constrained by some step response performance indicators. Three case studies have been taken as benchmarks, and results show that this strategy is promising.