The evidence base for micronutrient powder (MNP) interventions predominantly consists of quantitative studies focused on measuring coverage, utilization, and/or biological outcomes. We need other types of studies to broaden the scope of our knowledge about determinants of MNP programme effectiveness. Addressing this knowledge gap, this paper focuses on the process of designing an ethnographic research protocol to obtain caregivers' perspectives on the factors that influenced their use of intervention delivery services and their adherence to MNP recommendations. The research was undertaken within the context of formative evaluations conducted in Mozambique and Ethiopia. Ethnography provides a means for acquiring and interpreting this knowledge and is an approach particularly well suited for formative evaluation to understand the response of a population to new interventions and programme delivery processes. We describe decisions made and challenges encountered in developing the protocol, and their implications for advancing methodology in implementation research science. In addition to a core team of three investigators, we added an “advisory group” of 10 experts to advise us as we developed the protocol. The advisory group reviewed multiple drafts of the interview protocol and participated in mock interviews. In the protocol development process, we faced the issues and made decisions about concerned gaps in content, cultural adaptations and comprehension, and interview guide structure and format. Differences between the core team and the advisory group in methodological approaches to the structure and content of questions call attention to the importance of establishing greater communication among implementation scientists working in nutrition interventions.