Climate change impacts increase pressure on challenges to sustainability and the developmental needs of cities. Conventional, “hard” adaptation measures are often associated with high costs, inflexibility and conflicting interests related to the dense urban fabric, and ecosystem-based adaptation (EbA) has emerged as a potentially cost-efficient, comprehensive, and multifunctional approach. This paper reviews and systematises research on urban EbA. We propose an analytical framework that draws on theory from ecosystem services, climate change adaptation and sustainability science. It conceptualises EbA in terms of five linked components: ecological structures, ecological functions, adaptation benefits, valuation, and ecosystem management practices. Our review identified 110 articles, reporting on 112 cities, and analysed them using both quantitative statistical and qualitative content analysis. We found that EbA research in an urban context is fragmented due to different disciplinary approaches and concepts. Most articles focus on heat or flooding, and the most studied ecological structures for reducing the risk of such hazards are green space, wetlands, trees and parks. EbA is usually evaluated in bio-geophysical terms and the use of economic or social valuations are rare. While most articles do not mention specific practices for managing ecological structures, those that do imply that urban EbA strategies are increasingly being integrated into institutional structures. Few articles considered issues of equity or stakeholder participation in EbA. We identified the following challenges for future EbA research. First, while the large amount of data generated by isolated case studies contributes to systems knowledge, there is a lack of systems perspectives that position EbA in relation to the wider socio-economic and bio-geophysical context. Second, normative and ethical aspects of EbA require more thought, such as who are the winners and losers, especially in relation to processes that put people at risk from climate-related hazards. Third, there is room for more forward-looking EbA research, including consideration of future scenarios, experimentation in the creation of new ecological structures and the role of EbA in transformative adaptation.