BACKGROUND: The prevalence of acute malnutrition is often high in emergency-affected populations and is associated with elevated mortality risk and long-term health consequences. Increasingly, cash transfer programmes (CTP) are used instead of direct food aid as a nutritional intervention, but there is sparse evidence on their nutritional impact. We aim to understand whether CTP reduces acute malnutrition and its known risk factors. METHODS/DESIGN: A non-randomised, cluster-controlled trial will assess the impact of an unconditional cash transfer of US$84 per month for 5 months, a single non-food items kit, and free piped water on the risk of acute malnutrition in children, aged 6-59 months. The study will take place in camps for internally displaced persons (IDP) in peri-urban Mogadishu, Somalia. A cluster will consist of one IDP camp and 10 camps will be allocated to receive the intervention based on vulnerability targeting criteria. The control camps will then be selected from the same geographical area. Needs assessment data indicates small differences in vulnerability between camps. In each trial arm, 120 households will be randomly sampled and two detailed household surveys will be implemented at baseline and 3 months after the initiation of the cash transfer. The survey questionnaire will cover risk factors for malnutrition including household expenditure, assets, food security, diet diversity, coping strategies, morbidity, WASH, and access to health care. A community surveillance system will collect monthly mid-upper arm circumference measurements from all children aged 6-59 months in the study clusters to assess the incidence of acute malnutrition over the duration of the intervention. Process evaluation data will be compiled from routine quantitative programme data and primary qualitative data collected using key informant interviews and focus group discussions. The UK Department for International Development will provide funding for this study. The European Civil Protection and Humanitarian Aid Operations will fund the intervention. Concern Worldwide will implement the intervention as part of their humanitarian programming. DISCUSSION: This non-randomised cluster controlled trial will provide needed evidence on the role of unconditional CTP in reducing the risk of acute malnutrition among IDP in this context. TRIAL REGISTRATION: ISRCTN29521514 . Registered 19 January 2016.