Children and adolescents’ mental health risk and resilience arise from a complex interplay of factors on several socio-ecological levels. However, little is known about the factors that shape the mental health of refugee youth living in refugee camps close to ongoing conflict. We conducted a cross-sectional study with a representative sample of 217 Burundian refugee children aged 7–15 and their mothers residing in refugee camps in Tanzania to investigate associations between risk, protective and promotive factors from various ecological levels (individual, microsystem, exosystem), and children’s post-traumatic stress disorder (PTSD) symptoms, internalizing and externalizing problems, and prosocial behavior. Data were collected using structured clinical interviews and analyzed using multiple regression models. Exposure to violence across all contexts and engagement coping were risk factors for PTSD symptoms and internalizing problems, while only violence by mothers seemed to increase children’s vulnerability for externalizing problems. A differential impact of violence exposures on prosocial behavior was observed. Higher-quality friendships appeared to protect youth from PTSD symptoms and externalizing problems, while they also promoted children’s prosocial behavior, just as mothers’ social support networks. Prevention and intervention approaches should integrate risk, protective and promotive factors for refugee youth’s mental health across multiple ecological contexts and take into account context-specific and adaptive responses to war and displacement.