Background: mRNA vaccines against SARS-CoV-2 have proven highly effective in reducing severe disease and death, but repeated administration induces an unusual shift in IgG subclasses. In particular, increases in IgG2 and IgG4 raise questions about their regulation, persistence, and implications for protective immunity. Methods: To investigate the longitudinal dynamics and factors influencing IgG subclasses and their impact on protective immunity, we analyzed the levels of IgG1–4 subclasses, C1q, and FcγR-binding IgG against antigens from multiple SARS-CoV-2 variants in a well-characterized cohort of healthcare workers in Spain. Results: Subclass responses were shaped by exposure history, with infection before vaccination limiting the extent of IgG2 and IgG4 class switching relative to infection after vaccination. IgG4 demonstrated broader reactivity to Omicron variants than IgG1, and both IgG2 and IgG4 showed slower decay of circulating antibody levels than IgG1. IgG4 levels correlated with FcγR- and C1q-binding antibodies only in participants with lower IgG1, suggesting competition between subclasses. During Omicron predominance, elevated IgG2 and IgG4 were linked to increased risk of breakthrough infection in vaccinees, whereas levels of IgG1 and FcγR- and C1q-binding antibodies were associated with protection. Conclusions: Our findings highlight marked differences in IgG subclass profiles according to first exposure history and suggest that IgG subclass distribution and persistence may influence antibody-mediated immunity following mRNA vaccination. Further studies are warranted to clarify the mechanistic and clinical implications of IgG subclass shift for long-term protection.