While it has been known for many years that children under five years old are much more vulnerable to most infectious diseases than older children or adults, we know very little about the specific immunological reasons. Thus, we leveraged our recently developed tonsil organoid model, a high-resolution in vitro system of human immunity to vaccination, to compare tonsils from children as young as 2 years old to those from young adults. After stimulation with the live attenuated influenza vaccine, toddlers exhibited lower levels of influenza-specific IgA and IgG antibodies, limited T-independent response, and fewer activated cytotoxic CD8+T cells, all critical components supporting influenza defense. Additionally, toddlers showed reduced levels of key cytokine signaling proteins, including FLT3L, IL2, IL17, TACI, which are important in antibody class switching. Conversely, toddlers produced more of the pro-inflammatory cytokines CCL2 and PAI1, both associated with more severe influenza infection. We observed fewer interactions between T and B cells and diminished TLR and T-bet signaling in toddlers than in adults. Further analysis identified distinct metabolic disadvantages in toddlers, particularly within germinal centers, observed in a time-dependent manner. Machine learning analyses of our multi-omic data highlighted dominant variables and key predictors that distinguish diverse immune responses among groups. Our study used systems approaches to underscore critical deficits in cellular compositions, cytokine profiles, intracellular signaling, cell-cell interactions, and metabolic programs in young children´s immune systems under vaccine/viral stimulation, offering valuable guidance for future vaccine development and therapies.