Because of their potential energy savings, thermally coupled distillation sequences provide interesting alternatives to the use of sequences based on conventional distillation columns. Three thermally coupled structures have been particularly analyzed for the separation of ternary mixtures: the sequence with a side rectifier, the sequence with a side stripper, and the Petlyuk column. Design methods have been developed for such sequences, but their dynamic and operational characteristics still require a wider understanding to promote their practical implementation. Previous works have shown that thermally coupled systems can provide suitable control properties; most of the studies on closed-loop control analysis of thermally coupled systems have been based on proportional-integral (PI) controllers. In this work, a PI controller with dynamic estimation of uncertainties is implemented for the control of the thermally coupled distillation arrangements. The controller comprises three feedback terms: proportional, integral, and quadratic actions. The last term provides a dynamic estimation of unknown load disturbances to improve the closed-loop performance. Comparison with the classical PI control law was carried out to analyze the performance of the proposed controller in facing unknown load disturbances in feed composition and set point changes. The results show that the implementation of the controller with dynamic estimation of uncertainties improved noticeably the closed-loop responses provided by the PI controller.