The COVID-19 vaccinations have played a significant role in controlling the pandemic. To elucidate their impact on the immune system, a COVID-19 vaccination atlas was developed using an integrative systems vaccinology approach. The atlas includes 562 samples from 245 participants, including both healthy individuals and those infected with or without prior vaccination, and covers the administration of five vaccines in different regimens. Key findings include the identification of distinct immune markers that differentiate between vaccine types and infection statuses. We observed that mRNA vaccines induced transient but strong immune responses after booster doses, whereas viral vector vaccines showed sustained immune activation with infection, partially resembling the immune profile exhibited during infection. Heterologous vaccination regimens demonstrated enhanced immune diversification compared to homologous regimens. Finally, we described the immunological landscape of COVID-19 vaccines and vaccines against other pathogens, at the gene-level and in cell population dynamics.