The evaluation of the strategic supply chain configuration is considered one of the strategic logistics decisions, especially in food assistance supply chains focused on generating better nutritional conditions in vulnerable populations. In Colombia, there is a social program called Bienestarina, which aims to promote food and nutritional security in a vulnerable population. Although the government supports the program for improving nutritional support, there are currently inconsistencies in freight flows, lack of coverage in some areas, and delivery delays. Therefore, this work aims to evaluate the current configuration of the supply chain and propose improvements related to the facility location. Such advances would enable the increase in the efficacy of the network and the reduction of malnutrition in the country. For this purpose, a mixed-integer mathematical programming model is presented, which considers the weighted distance criterion for different demand scenarios and supports the location-allocation decision in a social assistance supply chain. The current network configuration was compared with the optimal proposed structure. The comparisons show highly potential improvements in freight flow allocation, suggests several variations in the existing warehouses emplacement, and generates public policy implications to reduce the logistic cost in the system, prioritizing in turn the demand covering.