Proteins are an effective platform for vaccine design by enabling multivalent antigen presentation and stabilizing antigen structures to enhance immunogenicity. This study investigates the molecular design and ability to position antigens on self-assembled protein nanocages (SAPNs) as a universal influenza vaccine, incorporating highly conserved nucleoprotein peptides (NP55-69 and NP147-158) as CD4+ and CD8+ T cell antigens alongside hemagglutinin stalk (HrHA) and matrix protein 2 ectodomain (4M2e). The SAPNs display HrHA and 4M2e on their external surface while embedding NP antigens internally. The engineered SAPNs feature a modular design, enabling precise antigen placement and enhanced accessibility through optimized linker length. This nanostructure elicited robust cellular and humoral immune responses in mice, including cross-reactive antibodies and antigen-specific T cell activation. These findings highlight the potential of SAPNs as a versatile platform for universal influenza vaccine development and the role that protein design plays in the spatial organization of self-assembled protein materials and its effect on biomedical function.