Community-based projects with inclusive stakeholder engagement are increasingly important to achieve robust outcomes in the science and management of ‘wicked’ urban ecosystem service challenges. We summarize lessons learned from a transdisciplinary, team-based doctoral education program that engaged students in research on such multi-stakeholder, complex problems. The key lessons are (a) problem-based projects foster active student engagement and accelerate transdisciplinary analysis, (b) problems addressing more acute interventions by public or private organizations enable learning by clearly delineating the issues and revealing the goals and perspectives of varied stakeholders, (c) successful projects that address wicked problems require that transdisciplinary teams begin from inception to robustly frame research questions with multiple lenses and choose appropriate theories and methods to implement projects, (d) regular stakeholder engagement leads to mutually meaningful project outcomes that advance scholarly frontiers for university researchers and provide relevant solutions for community partners, and (e) university administrative investment in program faculty, students, and staff and flexibility to reward innovative collaborations across disciplinary boundaries are keys to facilitate success in transdisciplinary education. Our lessons provide guidance both for addressing wicked problems through research projects in general and for formulating transdisciplinary training approaches for graduate education.