Childhood malnutrition is highly prevalent and associated with high mortality risk. In observational and interventional studies among malnourished children, body composition is increasingly recognised as a key outcome. The deuterium dilution technique has generated high-quality data on body composition in studies of infants and young children in several settings, but its feasibility and accuracy in children suffering from moderate acute malnutrition requires further study. Prior to a large nutritional intervention trial among children with moderate acute malnutrition, we conducted pilot work to develop and adapt the deuterium dilution technique. We refined procedures for administration of isotope doses and collection of saliva. Furthermore, we established that equilibration time in local context is 3 h. These findings and the resulting standard operating procedures are important to improve data quality when using the deuterium dilution technique in malnutrition studies in field conditions, and may encourage a wider use of isotope techniques.