Transdisciplinary research and collaboration is widely acknowledged as a critical success factor for solution-oriented approaches that can tackle complex sustainability challenges, such as biodiversity loss, pollution, and climate-related hazards. In this context, city governments’ engagement in transdisciplinarity is generally seen as a key condition for societal transformation towards sustainability. However, empirical evidence is rare. This paper presents a self-assessment of a joint research project on ecosystem services and climate adaptation planning (ECOSIMP) undertaken by four universities and seven Swedish municipalities. We apply a set of design principles and guiding questions for transdisciplinary sustainability projects and, on this basis, identify key aspects for supporting university–municipality collaboration. We show that: (1) selecting the number and type of project stakeholders requires more explicit consideration of the purpose of societal actors’ participation; (2) concrete, interim benefits for participating practitioners and organisations need to be continuously discussed; (3) promoting the ‘inter’, i.e., interdisciplinary and inter-city learning, can support transdisciplinarity and, ultimately, urban sustainability and long-term change. In this context, we found that design principles for transdisciplinarity have the potential to (4) mitigate project shortcomings, even when transdisciplinarity is not an explicit aim, and (5) address differences and allow new voices to be heard. We propose additional guiding questions to address shortcomings and inspire reflexivity in transdisciplinary projects.