Different thinking and strategies are needed to transform our food systems at different scales. Food systems can be changed towards a more sustainable path through multi-stakeholder transformative governance at the landscape level because that is where national-level visions, objectives, and policies meet with local practice, priorities, and actions. Concrete and practical guidance on how to effectively put a multi-stakeholder transformative governance process into practice is missing. Through the Global Environment Facility (GEF) funded ‘Food Systems, Land Use and Restoration Impact Programme’, led by the World Bank, countries are supported in integrated landscape management (ILM) to ensure that production systems are embedded within wider landscapes to safeguard the natural capital and ecosystem services on which they depend. A customised methodology to assess and measure the effectiveness of ILM-relevant multi-stakeholder transformative governance, incorporating right-based planning and tenure aspects, has been developed that makes governance explicit in the ILM process. This methodology aims to improve landscape-level institutional coordination, coherence, and collaboration through enhanced horizontal and vertical coordination and network dynamics. The conceptual framework of the customised methodology and how to operationalise it are explained and illustrated with the application in the country projects in Kenya, Nigeria, and Viet Nam. Making transformative governance explicit within the ILM process at the landscape level will require investments in time and capabilities, but allows governance to act as a catalyst towards more sustainable pathways.