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BACKGROUND: Linear growth failure is the most common form of undernutrition. Childhood stunting impairs human development and health and productivity in adulthood. Ethiopia has a high prevalence of stunting, with diets reliant on staple crops with low nutrient content. Maize is the most highly produced crop in Ethiopia. Unfortunately, conventional maize has poor protein quality due to a poor balance of essential amino acids. Quality protein maize (QPM) varieties are biofortified with these essential amino acids and, in controlled trials, improve child growth. However, evidence on the impact of QPM adoption and consumption on protein status and linear growth of children under natural circumstances is not yet available. METHODS/DESIGN: A randomized controlled trial was carried out to evaluate the impact of a) nutrition-focused adoption encouragement and provision of QPM seed in small seed packs, and b) a consumption encouragement intervention primarily targeting female caregivers and encouraging earmarking and integration of QPM into diets for infants and young children. The trial (n = 1611) had three randomly assigned arms: a control group; a first intervention group receiving adoption encouragement only; and a second intervention group receiving both adoption and consumption encouragement. The primary outcomes of this study are QPM consumption, protein status, and linear growth of children, assessed using questionnaires, biological specimen collection, and anthropometry over one cycle of agricultural production and post-harvest consumption. Secondary outcomes include child stunting, acute malnutrition, underweight, total intake of utilizable protein, and caregivers' cooking and child feeding practices. DISCUSSION: This study addresses important behavioral barriers between the development of a biofortified crop, QPM, and its impact on children's nutrition and health in a natural setting. The randomized controlled trial design, collection of data in multiple domains along hypothesized impact pathways, and assessment of nutritional status using both biomarkers and anthropometry allow greater understanding on mechanisms of impact. This trial is the first such study to be conducted with a biofortified staple crop in a natural setting and supports the Government of Ethiopia's current targets for nutrition and agriculture. PROTOCOL REGISTRATION NUMBER: Prospectively registered in the AEA RCT Registry (AEARCTR # 0000786) on 24 July, 2015, and retrospectively registered on ClinicalTrials.gov (NCT02710760) on 30 January, 2016.