Metropolitan areas are highly complex systems where a transition towards food security encompasses a systematic change in the whole food chain. Existing decision support tools that have been developed to inform policy-makers are mostly data-driven but hardly consider the activities and preferences of different stakeholders in the food system. The aim of this article is to contribute to urban food security by combining stakeholder participation with model-driven decision support. For this purpose, we developed and tested the Transition Support System (TSS) approach. In this TSS approach, decision support tools and participatory processes are mutually employed to promote urban food security in an ongoing, stakeholder-inclusive and reflexive process of governance. Our application of the TSS approach in two contrasting case studies highlights how this can contribute towards the development of new perspectives on urban food security, building a joint agenda towards the future and better (mutual) understanding of the issues at stake. We conclude that promoting a transition in the urban food system demands joint learning and reflexive evaluation in order to adapt governance, requiring researchers to play a supporting role in a broader process of change.