While there has been significant progress regarding the research mode ''transdisciplinary research'' (TDR) on a theoretical level, case studies describing specific TDR processes and the applied methods are rare. The aim of this paper is to describe how the first phase (Phase A) of a TDR project can be carried out in practice and to evaluate its accomplishments and effectiveness. We describe and evaluate Phase A of a TDR project that is concerned with tipping points of riparian forests in Central Asia. We used a TDR framework with objectives for Phase A and selected a sequence of methods for transdisciplinary knowledge integration. Semi-structured expert interviews for eliciting problem perceptions prepared for two transdisciplinary workshops, in which perception graphs, interest-influence diagrams and stakeholder network analyses were applied in addition to discussions in the plenary and in break-out groups. Scientists and stakeholders achieved to jointly frame the real-world problem, formulate research objectives, design a framework for knowledge integration, build a TDR team and decide on specific research activities for the main project phase. TDR context, process and products were judged by workshop participants positively, with average ratings above 3 on a scale from 0 (worst) to 4 (best). Strengths of our particular TDR approach during Phase A were the direct contact (interviews and two workshops) with potential TDR participants and the ability to allocate sufficient time and money to Phase A due to the funded project pre-phase of 1 year. TDR in countries foreign to the scientists, as in our study, is hampered by language barriers as well as by a lack of familiarity with local conditions, in particular regarding stakeholder interrelations that cannot be simply overcome by a stakeholder analysis. We believe that the presented approach for setting up a TDR project can serve as a good basis for the design of other projects.