This work presents an algorithmic approach to allow for the integrated design of processes and their control systems taking into account the controllability and the stability properties of the resulting system. The application of the proposed method has been carried out taking as an example model an alternative configuration to an Activated Sludge Process belonging to real wastewater treatment plant. In the integrated design, the process parameters are evaluated simultaneously with the parameters of the control system by solving a constrained non-linear optimisation problem. The considered cost function includes the investment and the operation costs and the constraints are selected to ensure that the values of some controllability and stability measures of the resulting system, are within specified ranges. These measures consist of the closed loop disturbances gains (CLDG) and the eigenvalues of some close-loop transfer matrices.