My PhD research seeks to explore the dynamics of differential empowerment of civil society organisations throughout the European Union accession process of three different countries: Croatia, Montenegro, and Serbia. This case study presents my use of process-tracing as a key method in establishing a link between the usage of European Union-related opportunities and domestic empowerment. It discusses how a combination of different qualitative methods – semi-structured interviews, participant observation, and documentary analysis – can facilitate the filling of evidentiary gaps in a process-tracing approach. Particular attention is given to the treatment of non-linear, protracted or evolving processes. Finally, the case study sheds light on the methodological challenges I faced in applying process-tracing not to a single case, but in a comparative setting.