Even though vaccines protected many from infection, not all were protected, and vaccinated individuals displayed a wide range of clinical outcomes, from complete protection against infection to multiple breakthrough infections. This study aimed to identify baseline differences following identical ChAdOx1/ChAdOx1/BNT162b2 in infection-free and breakthrough-infected individuals to find molecular signatures linked to enhanced SARS-CoV-2 protection. Samples from a previous longitudinal study were analyzed, classifying subjects as 'Protected' or 'Infected' based on infection status over two years. SARS-CoV-2-specific immunological assays and single-cell RNA sequencing evaluated baseline differences. Although humoral response measurements showed no significant difference, enhanced cellular responses via enzyme-linked immunospot assays were observed in the Protected group. Differentially expressed genes and pathway analysis of T/NK subsets showed the Infected group had reduced inflammation and interferon responses. The Infected group also displayed downregulated interaction with CD4+ T cells. B subset analysis revealed more memory B cells in the Infected group, accompanied by downregulation of immune regulatory genes and upregulation of the small ubiquitin-related modifier pathway. Our findings revealed differential molecular signatures in the baseline immune subsets of vaccinated individuals with prolonged protection and breakthrough infection. Reduced immune regulation and altered cell interactions may contribute to breakthrough infection, providing insights for future vaccine development and targeted protective strategies.