This article discusses methodological issues associated with education research in Bosnia and Herzegovina (BiH) and describes strategies taken to address them. Within a case study, mixed methods allowed the author to examine school leaders' perceptions multi-dimensionally. Multi-level analysis was essential to the understanding of policy-making and implementation in BiH, where school governance was affected by the political dynamics beyond local communities. In the research operation phase, multiple measures were taken to facilitate the implementation process, counter validity threats and solicit respondents' participation in a politically charged and fragmented post-conflict society. Data analysis was conducted by following established procedures, while requiring a careful synthesis of mixed-methods results. By making explicit various methodological issues that were encountered and describing strategies adopted, this article intends to contribute to the improvement of and discussion around research design and implementation in similarly challenging post-conflict environments. (Contains 5 notes.)