This paper presents a methodological framework to analyse sustainability innovations in the water–energy–food nexus and strategies for governing transition processes towards their widespread implementation. An application to a case study in Cyprus shows the interrelations of several sustainability innovations in the water, energy and food sectors, and specific learning requirements that need to be addressed to achieve a transition towards sustainable development. The framework helps to explore systematically responsibilities of different stakeholders for the implementation of innovations and thereby provides critical information for reflexive governance processes.