In this paper we present a novel methodology for identifying stakeholders for the purpose of engaging with them in transdisciplinary, sustainability research projects. In transdisciplinary research, it is important to identify a range of stakeholders prior to the problem-focussed stages of research. Early engagement with diverse stakeholders creates space for them to influence the research process, including problem definition, from the start. However, current stakeholder analysis approaches ignore this initial identification process, or position it within the subsequent content-focussed stages of research. Our methodology was designed as part of a research project into a range of soil threats in seventeen case study locations throughout Europe. Our methodology was designed to be systematic across all sites. It is based on a snowball sampling approach that can be implemented by researchers with no prior experience of stakeholder research, and without requiring significant financial or time resources. It therefore fosters transdisciplinarity by empowering physical scientists to identify stakeholders and understand their roles. We describe the design process and outcomes, and consider their applicability to other research projects. Our methodology therefore consists of a two-phase process of design and implementation of an identification questionnaire. By explicitly including a design phase into the process, it is possible to tailor our methodology to other research projects.