Summary Quantum dot (QD) barcoded microbeads are a promising technology for high-throughput biodetection applications. Here we developed QD barcodes of a novel formulation to improve the bead stability, fluorescence consistency, targeting agents loading, and analytical sensitivity as well as to simplify the conjugation process. This novel formulation contains a mixed-polymer system in preparing the barcodes and a seed-mediated strategy to grow metal nanoshells on the surface of QD barcodes. The newly designed barcodes exhibited enhanced stability and a two-order improvement in analytical sensitivity compared with barcodes without any metal coating. This sensitivity enabled the barcodes to be used for multiplexed biosensing, for example, to differentiate the deadly malaria pathogen strain Plasmodium falciparum from the less lethal Plasmodium vivax specie in a single vial. Such improvements in QD barcodes properties will allow this multiplexed detection platform to emerge from academic development into broad practical applications.