The binary mixture formed by acetonitrile (MeCN) and water (H2O) presents a minimum azeotrope highly sensitive to pressure variations, which can be separated through pressure-swing distillation (PSD), which is considered a very energy efficient process due to the possibilities of heat integration, in particular integration between the condenser and the reboiler of columns, known as Fully Heat-Integrated PSD (FHIPSD); in addition to being friendly from the environmental point of view. Despite promoting energy gains, integration reduces the freedom to control the process and, consequently, allows pressure fluctuation in the high-pressure column. This study evaluates the use of a partially flooded reboiler/condenser as a way to recover a degree of freedom of the process. The ability to maintain the purity specifications of products in two FHIPSD control configurations (conventional and with partially flooded reboiler/condenser) was evaluated for disturbances in the flow rate and feed composition. The use of a partially flooded reboiler/condenser allows controlling the heat exchange area by manipulating the level of liquid in the heat exchanger. The results showed that the partially flooded reboiler/condenser configuration promoted significant reductions in the steady state error values in the MeCN composition; and for positive flow disturbances, the steady state error value was reduced from 0.109 mol% to 0.004 mol%.