As nanomaterials (NMs) possess attractive physicochemical properties that are strongly related to their specific sizes and morphologies, they are becoming one of the most desirable components in the fields of drug delivery, biosensing, bioimaging, and tissue engineering. By choosing an appropriate methodology that allows for accurate control over the reaction conditions, not only can NMs with high quality and rapid production rate be generated, but also designing composite and efficient products for therapy and diagnosis in nanomedicine can be realized. Recent evidence implies that microfluidic technology offers a promising platform for the synthesis of NMs by easy manipulation of fluids in microscale channels. In this Review, a comprehensive set of developments in the field of microfluidics for generating two main classes of NMs, including nanoparticles and nanofibers, and their various potentials in biomedical applications are summarized. Furthermore, the major challenges in this area and opinions on its future developments are proposed.