Co-circulation and re-emergence of antigenically related viruses such as dengue (DENV), Zika (ZIKV), and yellow fever (YF) in the Americas has brought a sense of urgency in the field to further define the genesis and to more fully describe the immune response. The recent explosive epidemics of Zika in the Americas and the co-circulation of ZIKV with the phylogenetically similar DENV has raised important questions and concerns regarding the role of cross-reactive immunity in protection and potential enhancement of severity of subsequent ZIKV or DENV infections in pre-immune individuals and the safety of vaccines against both viruses in endemic populations. Antibodies are a critical part of the immune response for clearing flavivirus infections, but the role of pre-existing antibodies in protection or enhancement of subsequent infection and disease with closely related viral species and strains is still not fully understood. We have developed a novel Multi-Color FluoroSpot (MCF) assay based on our ELISPOT-derived assay, previously designated the Quad-color FluoroSpot (QCF), in order to study the development of type-specific versus cross-reactive responses within the B cell pool of Zika virus (ZIKV)- and/or dengue virus (DENV)-infected patients. The QCF is based on a panel of four fluorescent Qdots, each conjugated to a monoclonal antibody specific to one of the four DENV serotypes; now we have included a fifth color (Qdot) for ZIKV to enable analysis of the specificity versus cross-reactivity of B cell populations at a single-cell level for all four DENV serotypes and ZIKV. This novel assay allows us to analyze unique human samples from long-term studies of dengue and Zika in Nicaragua to investigate the nature of B cell/antibody responses and their role in pathogenesis and/or protection in secondary flavivirus infections and could have important implications for vaccine development for Zika and dengue.