This paper utilises the ‘sustainable innovation journeys’ concept to trace how people organise and design urban food initiatives and influence city-region food policy. We evaluate whether designs succeed or fail and monitor the exchange of ideas that takes place between stakeholders. Tracing these interactions reveals the transformative potential of innovative projects, particularly if the food system changes they bring to the fore are aligned with policy interests. Three case studies provide on-the-ground insights to assess how small and medium-sized enterprises at the micro-level induce sustainability shifts. The case studies are businesses in the city-regions of Rotterdam, The Netherlands (urban farm and circular food economy); Vigo, Spain (food, forest and multi-functional land use); and Zurich, Switzerland (organic food and short supply chains). Each initiative was studied in-depth over a two-year period, with follow-up analysis for a further four years to monitor change over time (2013–2018). The cases promote the adoption of micro-level innovation practices: locally designed transition pathways that bring the benefits of change to the city-region (i.e. from the micro-level initiative to meso-level policy). The analysis highlights the importance of ‘soft change’. This can be something as simple as visiting an inspiring urban food initiative and meeting with stakeholders to generate mutual understanding, from where interests align to influence food chain practices and policy. Soft changes act as ‘seeds of transition’ for a shift towards more sustainable urban food systems, but we observe too potentially negative impacts due to lack of alignment at the micro- (initiative) or meso- (city-region) levels.