Acute malnutrition in children under 5 years is persistent in Eastern Africa's arid and semiarid lands. This study aimed to identify the drivers of acute malnutrition in Turkana and Samburu counties, Kenya. This was a population-based longitudinal mixed-methods observational study. Qualitative and quantitative data were collected at Wave 1, but only quantitative data were collected during follow-up. Participants were a representative sample of children and their primary caregivers from households with children under 3 years at Wave 1. Anthropometric measurements of all children under 5 years in the sampled households were taken at Wave 1 (May to July 2021), and one child under 3 years was randomly selected for follow-up about every 4 months over 2 years for six data collection waves. The study also collected data on sociodemographics; child feeding practices and morbidity; household water and food insecurity; shocks; coping strategies, social safety nets and economic safeguards; water, sanitation and hygiene; women's decision-making and food consumption. Qualitative data were collected through community dialogues, focus group discussions, in-depth interviews, photovoice and key informant interviews with mothers and fathers with children under 5 years, community leaders, county officials and staff of nongovernmental organisations. Data collection is complete and analysis is ongoing. The analysis includes thematic analysis of qualitative data and descriptive and multi-variable regression analyses of quantitative data.