Climate change increasingly stresses water and energy systems, with cascading effects on food production and nutritional outcomes. This study uses an integrated WEF nexus modelling framework to evaluate how different climate scenarios influence environmental footprints (water, energy, greenhouse gas emissions), food availability, nutrient supply, and health risks associated with undernutrition. We apply the model to a representative agro ecological region, simulating three climate change futures (low, moderate, and high warming) and intervention policies (e.g. irrigation efficiency, renewable energy for pumping, dietary shifts). Our results suggest that under the high warming scenario, blue water use increases by ~25%, energy demand for irrigation rises ~30%, and crop yields decline by 12–20%. Nutrient supply (protein, iron, vitamin A) falls 10–18%, pushing ~8% more of the population into undernutrition. Intervention scenarios mitigate many impacts: improved irrigation reduces water use by ~20%, renewable energy pumping cuts GHG emissions by ~40%, and moderate diet shifts maintain nutrient adequacy while reducing environmental burdens. This study underscores the need for integrated policies across water, energy, agriculture, and nutrition sectors to build resilient food–nutrition systems under climate change.