The granting of patents for agricultural plants and animals and breeding methods stirred a major controversy in Germany since 2003. While the agricultural ministry was the main addressee of the protests, the formal competence for patent law lies with the Ministry of Justice and the European Patent Office. At first sight, this appears as a clear instance of de-compartmentalisation of agricultural policy making. However, agricultural patents have never been the domain of agricultural policy-making. This observation challenges us to extend the analysis of policy de-compartmentalisation beyond the level of institutions to include policy networks and the communities of practice under a policy domain. This paper traces the policy process through which the controversy over agricultural patents unfolded between 2003 and 2013. The paper argues that ‘de-compartmentalisation’ is a useful heuristic strategy to analyse interwoven processes of change at the level of institutions, policy networks, and communities of practice.