Background/Objectives: Food system assessments in Sub-Saharan Africa have pre-dominantly focused on caloric availability, often overlooking the structural and nutri-tional quality of the food supply. This study aims to analyze long-term changes in caloric availability and the structure of the protein supply, focusing on adjusted protein density, the balance between animal and plant proteins, and the diversification of animal protein sources. Methods: The analysis is based on data from the Food and Agriculture Organization of the United Nations for the period 1961–2023, covering Nigeria, the Republic of the Congo, the Democratic Republic of the Congo, Kenya, South Africa and Ethiopia. A longitudinal approach was applied where data were available, complemented by a recent comparative analysis (2010–2023). Derived indicators include total protein supply, ad-justed protein density, the share of animal and plant proteins and the Her-findahl-Hirschman index (HHI) to assess the diversification of animal protein sources. Results: Findings show that increases in caloric availability are not consistently associated with improvements in adjusted protein density or nutritional quality. Significant dif-ferences are observed across countries in protein supply levels, structural composition, and diversification patterns. Results reveal heterogeneous trajectories of food systems, from diversified to structurally constrained or highly concentrated systems. Conclusions: Beyond caloric availability, the structure and quality of the food supply are essential for assessing food system performance. Quantitative gains alone do not ensure improved nutritional or sustainable outcomes. The study highlights the importance of considering protein supply structure, diversification and nutritional efficiency in the context of SDG 2 (Zero Hunger) and broader food system transformation.