Infection with the Zika virus (ZIKV) is an ongoing problem especially as accurate, cost-effective testing remains unresolved. In addition, coinfection occurs with both the Dengue virus (DENV) and ZIKV which leads to cross-reactivity between the flaviviruses and can result in false positives and inaccurate testing. This supports the current need for a simple assay that can detect Zika antibodies sensitively that at the same time can differentiate between cross-reactive antibodies. In this study, we developed customizable magnetic relaxation nanosensors (MRnS) conjugated to various ligands, which included ZIKV (ZENV, zika domain III and NS1) and DENV proteins for specific detection of cross-reactive Zika and Dengue antibodies. Binding interactions between functional MRnS and corresponding targets resulted in the change in spin-spin magnetic relaxation time (T2MR) of water protons, allowing for a rapid and simple means by which these interactions were detected and quantified. Our results show the detection of Zika antibodies within minutes at concentrations as low as 20 nM and display high specificity, reproducibility, and analytical sensitivity. Furthermore, a mixture of functional MRnS was used for the one-step simultaneous detection and differentiation of Zika and Dengue infections. These results demonstrate high specificity and sensitivity for the detection of ZIKV and DENV despite coinfections in both simple and complex media. Overall, our magnetic nanoplatform could be used as a rapid and sensitive assay for the detection of not only Zika- and Dengue-related testing but can be further applied to serological samples of any other pathogens.