BackgroundMalnutrition continues to be a public health challenge in sub-Saharan African countries. In Ethiopia, there is a paucity of data regarding factors affecting treatment outcomes in children with severe acute malnutrition (SAM).MethodsA prospective cohort study was conducted among children aged 6 to 59 months with SAM, receiving care at Jimma University Medical center, Ethiopia. Bivariate and multivariate analyses were computed to determine factors associated with treatment outcomes. Kaplan–Meier survival analysis, life-table analysis, and Log rank test were used to determine death rates, estimate the proportion of surviving, and compare time to recovery (nutritional cure).ResultsA total of 133 children were included in this study and 79.7% had medical comorbidities. Overall, nutritional recovery, death, and default rates were 25.6%, 3.8%, and 7.6%, respectively. There was no significant difference in the nutritional recovery rate (26.1% versus 25.4%; p=0.4) and the median time to recovery between children who had diarrhea at admission (26 days; 95% CI: 24.0–28.7) and those who had not (26.0 days; 95% CI: 21.90–30.10). Likewise, the average daily weight gain was not significantly different between the two groups (6.34 g/kg/day versus 7.76g/kg/day, p=0.4). Having diagnosed with tuberculosis (Adjusted Hazard Ratio (AHR)=0.19, CI 0.06–0.62) and anemia (AHR =0.32, CI 0.14–0.74) and treatment failures (AHR=0.17, CI, 0.16–0.03) were predicting factors for time to recovery.ConclusionThe recovery rate and average daily weight gain were found to be sub-optimal in the study population. However, the median time to recovery was within the national recommendation. There was no significant difference in the recovery rate and time to recovery between the two groups. Treatment failures and the presence of tuberculosis and anemia were indicators for prolonged stabilization phase and time to achieve nutritional cure. Optimal average daily weight gain and clinical management of comorbidities may enhance early recovery in hospitalised children with SAM.