A dynamic model for the Hybrid Heat-Integrated Distillation System (HHIDiS) incorporating a Heat and Mass Exchanger (HME) was developed. The system’s behaviour under PID control was simulated using Simulink/MATLAB, with a focus on examining the effects of industrial constraints, such as fouling growth on heat exchanger surfaces and liquid hold up within the plate HME on operational quality indices. Results revealed that increases in fouling resistance or liquid hold up alter the thermal inertia of the HME, condenser, and reboiler, subsequently impacting the dynamic performance of PID control loops. These effects were analysed by simulating the closed-loop HHIDiS system at varying stages of fouling accumulation and liquid retention. Changes caused by fouling and liquid hold up were reflected in control quality indices such as overshoot, peak time, delay time, rise time, and settling time. Such variations may compromise PID control effectiveness. The findings emphasise the need to adjust PID tuning parameters to maintain optimal control performance when industrial constraints shift. Adverse effects can be mitigated through periodic recalibration of PID gains. Simulation results demonstrated that the proposed HHIDiS system remains dynamically stable despite these challenges and that standard PID controllers are suitable for its operation. These insights highlight the importance of proactive control adjustments to sustain high performance under evolving industrial conditions.