Early-life antibiotic exposure leads to impaired antibody responses to vaccination in mice. To investigate whether this is the case in human infants, we prospectively followed 191 vaginally born, healthy, term infants from birth to 15 months. Antibiotic exposure, especially in the neonatal period, was associated with lower vaccine antibody responses, particularly those against pneumococcal polysaccharides in the PCV13 vaccine. Whole-blood RNA sequencing revealed that neonatal antibiotic exposure was associated with an inflammatory transcriptional profile pre-vaccination. Shotgun metagenomics also revealed reduced Bifidobacterium in stool samples of infants exposed to neonatal antibiotics at the time of primary immunisation, the relative abundance of which correlated with antibody responses at 7 months. Supporting a causal relationship, administration of a probiotic containing Bifidobacterium and Lactobacillus spp. restored impaired PCV13-specific IgG responses in germ-free mice. These data suggest that microbiota-targeted inventions may support better antibody responses to vaccination in infants with a disrupted microbiota.