Africa faces a rapidly increasing burden of non-communicable diseases (NCDs), including hypertension, type 2 diabetes mellitus, cardiovascular disease, obesity, and chronic kidney disease. While policy responses have traditionally focused on treatment, adult lifestyle modification, and health service expansion, insufficient attention has been directed toward the environments where future disease risk is created. One of the most overlooked of these environments is the school food system. This paper introduces the concept of metabolic debt, defined as the cumulative physiological burden generated by prolonged exposure to unhealthy dietary environments during critical developmental stages, resulting in future healthcare expenditure, productivity losses, and increased demand for chronic disease services. Across many African secondary schools, particularly boarding schools, adolescents are routinely exposed to diets dominated by refined carbohydrates, sugar-sweetened beverages, and ultraprocessed foods. Although these dietary patterns offer operational advantages, including cost efficiency, shelf stability, and procurement convenience, they may simultaneously contribute to the accumulation of metabolic debt. Using an illustrative Kenyan boarding school case study and applying the World Health Organization (WHO) Health Systems Building Blocks Framework, this paper argues that unhealthy school food environments represent upstream drivers of future Universal Health Coverage (UHC) expenditure. The paper concludes that school nutrition reform should be viewed as a strategic investment in health system resilience, economic productivity, and long-term disease prevention.