Fluorescent quantum dots have been used in biological applications as desirable fluorescent labels instead of traditional fluorophores. Incorporation into microspheres enhances many features of quantum dots that make them ideal for biological detection, such as photostability, multi-target, and improved brightness. Quantum dot-tagged microbeads are emerging as a new class of fluorescent labels and are expected to open new opportunities in nanotechnology and biology. In this review, we describe different approaches for the synthesis of quantum dot-tagged microbeads, surface modification methods that make microbeads suitable for bioconjugation, and the biological applications of the quantum dot-tagged fluorescent microbeads with their desired features in recent research. We also discuss the limitations of some kinds of quantum dot-tagged microbeads and the developments that will enhance their abilities in biological applications.