Fuel impurities, fed to a polymer electrolyte membrane fuel cell, can affect stack performance by poisoning of catalyst layers. This paper describes the dynamic behaviour of a stack, including state-of-the-art membrane electrode assemblies (MEA) of three different manufacturers, at different operating conditions. The voltage transients of the step responses to CO poisoning as well as air bleed recovery are compared, revealing differences in performance loss: slow poisoning versus fast recovery, incomplete recovery and voltage oscillation. The recorded behaviour is used to develop a model, based on Tafel equation and first order dynamic response, which can be calibrated to each MEA type. Using this model to predict voltage response, a controller is built with the aim of reducing the total amount of air bleed and monitoring upstream stack processes without the need of sensors measuring the poisoning level. Two controllers are implemented in order to show the concept from a heuristic, easy to implement, and a more technical side allowing more detailed analysis of the synthesis. The heuristic algorithm, based on periodic perturbations of the manipulated variable (air-bleed), is validated on a real stack, revealing a stabilized performance without the need of detailed stack properties knowledge.