BackgroundDuring humanitarian crises, women and children are particularly vulnerable to morbidity and mortality. To address this problem, integrated child health interventions that include support for the well-being of mothers must be adapted and assessed in humanitarian settings. Baby Friendly Spaces (BFS) is a holistic program that aims to improve the health and wellbeing of pregnant and lactating women and their children under two years of age by providing psychosocial support and enhancing positive infant and young child-care practices. Using a mixed-methods, pre-post design, this study explored ways to strengthen the implementation and acceptability of the BFS program, and assess outcomes associated with participation among South Sudanese mothers and their children living in the Nguenyyiel refugee camp in Gambella, Ethiopia.DiscussionA stronger evidence-base for integrated maternal and child health interventions, like BFS, in humanitarian emergencies is needed, but effectively conducting this type of research in unstable settings means encountering and working through myriad challenges. In this paper we discuss lessons learned while implementing this study, including, challenges related to ongoing local political and tribal conflicts and extreme conditions; implementation of a new digital data monitoring system; staff capacity building and turnover; and measurement were encountered. Strategies to mitigate such challenges included hiring and training new staff members. Regular weekly skype calls were held between Action Against Hunger Paris headquarters, the Action Against Hunger team in Gambella and Johns Hopkins’ academic partners to follow study implementation progress and troubleshoot any emerging issues. Staff capacity building strategies included holding brief and focused trainings continuously throughout the study for both new and current staff members. Lastly, we engaged local Nuer staff members to help ensure study measures and interview questions were understandable among study participants.ConclusionsResearch focused on strengthening program implementation is critically important for improving maternal and child health in humanitarian emergencies. Research in such settings demands critical problem-solving skills, strong supervision systems, flexibility in timeline and logistics, and tailor-made training for program and research staff members and context- adapted strategies for retaining existing staff.