The regular emergence of influenza strains with pandemic potential necessitates vaccines that elicit protective immune responses across genetically diverse human populations. A critical but understudied factor is how germline-encoded variation in immunoglobulin genes shapes the development of neutralizing antibodies. Here, by combining personalized immunoglobulin genotyping with high-throughput paired-chain antibody sequencing from influenza A hemagglutinin (HA)-binding B cells across four donors, using a technique we developed called individualized single-cell analysis of paired expressed antigen receptors (ISCAPE), we demonstrate that B cell responses to HA are highly individual. We identified a common IGHV2-70 polymorphism that impaired the function of a class of neutralizing HA head-directed antibodies. Furthermore, we described HA central stem-targeting broadly neutralizing antibodies that utilize IGHD3-3 recombined with diverse IGHV genes, expanding the known repertoire of stem antibodies and highlighting antibody gene usage population restrictions. We suggest that multi-donor repertoire studies, coupled with personalized immunoglobulin genotyping, can uncover germline-encoded functional variations and help mitigate population vulnerabilities in vaccine design.