Organic food markets substantially rely on a reliable control system. To identify and isolate the effect of different factors potentially influencing the uniform implementation of organic controls, we apply a stepwise estimation of different logit models. Using control data of German farms from five important control bodies we identify, first, risk factors for non-compliance of farms, second, the impact of the control body as well as, third, the potential impact of governmental institutions which are in charge for the implementation of the control system. The results indicate a need for a more harmonized implementation of the German organic control system.