Unconditional cash transfers (UCTs) are used to prevent acute malnutrition in emergencies but evidence on their effectiveness is lacking. In Niger, NGOs implemented annual UCTs with supplementary feeding during the June–September lean season, despite feeding programme admissions sometimes rising earlier. I hypothesised that starting the UCT earlier would reduce acute malnutrition prevalence in children 6-59 months old, but also, that this would promote early return of seasonal male labour migrants (exodants), limiting the effectiveness of the modified UCT. A cluster-randomised trial involved the poorest households receiving either the standard monthly UCT (June-September) or a modified UCT (April-September); both providing a total of 130,000 FCFA/£144. Pregnant and lactating women and children 6–<24 months old in beneficiary households also received supplementary food (June-September). We collected quantitative data from a cohort of households and children in March/April and October/November 2015 and conducted a process evaluation. The modified UCT did not reduce acute malnutrition prevalence compared with the standard UCT. Among beneficiaries in both arms the prevalence of GAM remained elevated at endline (14.7, 95%CI 12.9, 16.9), despite improved food security, possibly due to increased fever/reported malaria. Exode was highly prevalent (baseline population prevalence of short-term exode: 28.0, 95%CI 24.0, 32.4) and multi-annual, mostly to Libya. Probably because of distance and travel cost, the modified UCT did not affect exodant returns. Short-term exode was associated with greater odds of stunting (1.93, 95%CI (1.24, 3.00), P=0.003) and underweight (1.95, 95%CI (1.10, 3.45), P=0.021) among left-behind children. The greater odds of underweight persisted in exodant households recently receiving remittances (2.40, 95%CI (1.17, 4.92), P=0.017), suggesting remittances were inadequate. Non-food related drivers of malnutrition, including disease, may limit the effectiveness of UCTs to reduce acute malnutrition prevalence in Niger. Efforts to tackle undernutrition should consider the greater vulnerability of children in exodant households.