Today, tropical islands are on the frontline of climate change and have to overcome many challenges to improve food security. Circular food systems are required to become more self-sufficient and to limit environmental impacts. Livestock have a crucial role to play in a circular food system by valorising co-products, waste and rangelands and converting them into valuable food and manure. To facilitate the transition towards more circular systems, we propose a metabolism-based methodology, which aims to identify livestock-based scenarios to increase the circularity of food systems. The methodology enables three levels of accuracy and investment to cover the wide range of tropical island contexts. The three levels have the same objective but can be applied depending on the available data, time, funds and human resources. Level 1 is based on a proto-metabolism using macro data, level 2 on an accurate metabolism using a material flow analysis (MFA), and level 3 is a participatory approach based on stakeholder involvement in the metabolism. The methodology was applied to two case studies, Madagascar and Reunion island, which have similar soil-climate conditions but very different food systems. Level 1 was applied to Madagascar and theoretical and global levers are proposed such as increasing the livestock stocking rate to provide more recycling opportunities and more organic matter to be valorised. Due to the large size of the island and the diversity of productions and systems, further research is needed at sub-regional scale to identify complementary levers. In Reunion Island, levels 1, 2 and 3 were applied. Specific and local levers are proposed that were co-designed with local stakeholders such as co-composting livestock manure with green waste to produce organic fertilisers for sale to market gardeners.