Abstract Design disciplines have a long history of creating well-integrated solutions to challenges which are complex, uncertain and contested by multiple stakeholders. Society faces similar challenges in implementing the Sustainable Development Goals, so design methods hold much potential. While principles of good design are well established, there has been limited integration of design thinking with sustainability science. To advance this integration, we examine the process of designing MetaMAP: an interactive graphic tool for collaborating to understand social–ecological systems and design well-integrated solutions. MetaMAP was created using Research through Design methods which integrate creative and scientific thinking. By applying design thinking, researchers and practitioners from different backgrounds undertook multiple cycles of problem framing, solution development, testing and reflection. The testing was highly collaborative involving over 150 people from diverse disciplines in workshops, case studies, interviews and critique. Reflecting on this process, we discuss design principles and opportunities for integrating design thinking with sustainability science to help achieve Sustainable Development Goals.