The past decades have seen a rise of survey research in migration studies, which is often cross-national due to the very nature of migration. Conducting cross-country surveys presents challenges for researchers in terms of survey design, implementation, and data collection. A thematic focus on migration brings additional challenges due to the complexity of migration, issues of definitions, sampling and the geographical areas of interest. This paper gives insight into the practicalities of implementing a migration household survey in a developing country, conflict-affected setting. By focusing on these settings this paper is one of the few to target survey methodology in a non-developed country context. We highlight specific areas for attention within survey implementation stages: (1) scoping, (2) survey design, (3) training, (4) pilot, and (5) data collection. We specifically use the examples of the IS Academy project in Ethiopia and Burundi, hereby highlighting the differences between the two countries. The aim of this paper is to give practical guidelines for researchers and practitioners working in the area of migration research.