Background Undernutrition among children under five years of age continues to pose a critical public health challenge in low- and middle-income countries, especially in fragile and conflict-affected contexts such as Somalia. This study aims to estimate the prevalence of malnutrition and identify key socioeconomic, health-related, and environmental determinants associated with it among children under five in Afgoi District, Somalia.Methods A Facility-based cross-sectional study was conducted among 384 caregiver-child dyads recruited from two major health facilities in Afgoi District, Somalia, using consecutive sampling. Data were collected through standardized, face-to-face interviews and WHO-recommended anthropometric measurements to assess stunting, wasting, and underweight. Multivariable logistic regression analysis was performed to identify independent demographics, health-related, and environmental risk factors associated with under-malnutrition.Results This study revealed alarmingly high prevalence rates of undernutrition among children in Afgoi District: stunting (68.23%), wasting (58.33%), and underweight (86.72%), indicating coexisting chronic and acute nutritional deficiencies. Key socioeconomic and behavioral determinants identified included household income below USD 100 per month, suboptimal breastfeeding practices (particularly lack of exclusive breastfeeding), reliance on unsafe water sources, and high burden of infectious disease. Multi-variable logistic regression analysis demonstrated that exclusive breastfeeding was significantly protective against underweight (adjusted odds ratio [AOR] = 0.420; 95% CI: 0.205–0.862; P = 0.015), whereas access to unclean water was associated with a more than twofold increase in the odds of underweight (AOR = 2.225; 95% CI: 1.147–4.315; P = 0.019). Additionally, household income exceeding USD 300 per month was significantly associated with reduced odds of wasting (AOR = 0.323; 95% CI: 0.117–0.895; P = 0.034).Conclusion Undernutrition among children under five in Afgoi District is alarmingly prevalent and arises from a synergistic convergence of socioeconomic constraints, sub-optimal infant and young child feeding practices, particularly low coverage of exclusive breastfeeding, and environmental hazards, notably pervasive reliance on unsafe water sources. Effectively addressing this crisis requires urgent, coordinated multisectoral interventions: sustained, contextually grounded poverty reduction strategies; rigorous, behaviorally informed promotion of evidence-based feeding practices; equitable, climate-resilient expansion of safe water infrastructure; and systematic strengthening of primary health care systems to enhance integrated disease prevention, acute malnutrition management, and real-time nutritional surveillance.