This paper provided results of a framework-based self-reflection process conducted by the science and the practice leaders of two transdisciplinary projects realized in co-leadership from 2011 until 2014. It analyzes from the perspectives of the science and practice leaders for the whole research process including preparation, research, and follow-up phase, the (1) transdisciplinarity component of each module (in %); (2) outputs generated (tangible and intangible); (3) relevance of output for science and practice (qualitative ranking); (4) impacts emerging from the outputs (tangible and intangible); and (5) outcomes emerging from the impacts (tangible and intangible). Furthermore, the research process was reflected by practice and science project leaders and critical aspects identified. We found that first, a transdisciplinary research process might contribute to regional demands if it is carried out “timely.” Timeliness includes (1) the need from the perspective of the practice partners and the scientific community, (2) the willingness of the co-leaders to develop the project together, and (3) the fundamental organizational support. This was the case in our project where the results directly impacted the further development of the project. Second, a truly lived co-leadership consisting of clearly defined and lived roles and responsibilities, common definition and alignment of the goals, and acceptance of the differences in needs by practice and science leads to a trustful cooperation. Third, a good communication structure within the teams and between the practice and science teams allows to anticipating and overcoming problems at the practice-science interface leading to mutual learning and experience building. © 2015, The Author(s).