Complete mixing is hard to achieve in large bioreactors in wastewater treatment plants. This often leads to a non-uniform distribution of components such as dissolved oxygen and, hence, the process rates depend on them. Furthermore, when these components are used as input for a controller, the location of the sensor can potentially affect the control action. In this contribution, the effect of sensor location and the choice of setpoint on the controller performance were examined for a non-homogeneously mixed pilot bioreactor described by a compartmental model. The impacts on effluent quality and aeration cost were evaluated. It was shown that a dissolved oxygen controller with a fixed setpoint performs differently as a function of the location of the sensor. When placed in a poorly mixed location, the controller increases the aeration intensity to its maximum capacity leading to higher aeration costs. When placed just above the aerated zone, the controller decreases the aeration rate resulting in lower dissolved oxygen concentrations in the remainder of the system, compromising effluent quality. In addition to the location of the sensor, the selection of an appropriate setpoint also impacts controller behavior. This suggests that mixing behavior of bioreactors should be better quantified for proper sensor location and controller design.