In order to understand the professional conflicts concerning regional organic farming support policies, this article examines the institutional rifts visible in policy networks in five German and French regional cases (Hesse, Lower Saxony, Brittany, Auvergne, and the Rhône-Alpes region). The change in the scale of organic farming and the increase in the amount of public aid in this field, far from eliminating sectoral controversies, is fuelling competition between the professional bodies involved in developing and implementing policies. The comparative empirical survey conducted in Germany and France is based on an analysis of institutional archives and 40 semi-structured interviews with elected representatives and employees of professional representative bodies. Our study shows that the institutional conflicts identified in four out of five regional cases can only be understood at the crossroads between sectoral tensions and territorial configurations. On regional professional forums, organic farmers’ representatives are defending an alternative agricultural model against the dominant agricultural representatives who are trying to curb any protest. This dissension is common to all five regional cases. However, the conflicts within institutions manifest differently in different policy networks. The variety of fault lines that can crystallize in organic farmers’ representation as well as among the network of Chambers and those of specialist organic farming representatives attests to a territorial refraction of sectoral oppositions.