This article explores open-source visualization tools to enhance the understanding of small- and medium-enterprise (SME) ecosystem structures. Ecosystem approaches are becoming important in business strategy and innovation where organizations are heavily relying on inter-firm resources to innovate. Consequently, the traditional firm-focused business models face challenges, making it difficult for interconnected and diverse actors to co-create across firm boundaries. This challenge is even worse for manufacturing SMEs, who often lack the tools to make sense of their innovation ecosystem structures. We carried out a rich ethnographic investigation in three cases in the United Kingdom: the ceramic artist ecosystem, the 3D printing bureau ecosystem and the FabLab ecosystem. From the initial thematic analysis results, all actors highlighted the difficulty in understanding ecosystem networks. The following ecosystem attributes were identified as essential in understanding SME ecosystem structures: clusters and bridges, tie size, structural holes, role structure and interactivity. In this article, fourteen open-source visualization tools are tested to compare how well different tools reveal the six ecosystem attributes. Our findings demonstrate that open-source visualization tools have different affordances, most of which are useful in revealing ecosystem attributes. Results show that most visualization tools help aid the understanding of SME ecosystem structures. This study contributes new knowledge on the scarce subject of designing and managing ecosystems, presenting a unique approach to explore and understand ecosystem configurations. The study identifies limitations in open-source visualization tools and offers the design management community a set of recommendations for further development of visualization tools to support decision-making.