Researchers in multiple, related fields that address complex social and environmental challenges, have shown ongoing enthusiasm for applying transdisciplinary social-ecological systems (SES) research to promote sustainability. However, few studies have evaluated the effectiveness of SES approach, assessed its achievements, and identified challenges to its implementation toward knowledge production for environmental conservation. We report the results of a qualitative, participatory evaluation of several SES projects across Europe using an evaluation methodology tailored to transdisciplinary projects. We conducted 66 stakeholder interviews at four designated Long-Term Socio-ecological Research (LTSER) platforms – Danube Delta and Braila Island (Romania); Cairngorms (Scotland); and Doñana (Spain). Using qualitative analysis, we synthesized data from interviews and then returned to the sites to present findings to stakeholders in focus group discussions in order to incorporate their feedback into conclusions. We conclude that although particular scientists at each platform have taken on entrepreneurial roles to operationalize transdisciplinary science, a business-as-usual attitude tends to dominate institutions, limiting meaningful progress toward transdisciplinary objectives, including: integration of social science research, giving non-researcher stakeholders a more meaningful role in advancing relevant research, and improving knowledge exchange among different stakeholder groups, among other issues. While we found that all the components of transdisciplinary SES research exist at the sites, there is no overarching strategy to link long-term planning and funding, knowledge integration, and priority-setting with stakeholders to ensure the relevance of research for policy and practice. We conclude with reflections about implementing our evaluation methodology, and a call for periodic, participatory evaluation into the future.