Extracellular vesicles (EVs) present a promising modality for numerous biological and medical applications, including therapeutics. Developing facile methods to engineer EVs is essential to meeting the rapidly expanding demand for various functionalized EVs in these applications. Herein, we developed a technology that integrates enzymatic glycoengineering and microfluidics for effective EV functionalization. This method builds on a 3D nanostructured microfluidic device to streamline a multiple-step EV engineering process, which involves a step of enzymatic reaction to install azido-sialic acid residues to glycans on EVs using a sialyltransferase and an azide-tagged sialyl donor followed by the attachment of various functionalities, such as biotin and fluorescent labels, to the resulting azido-glycans on EVs through a biocompatible click reaction. Compared to traditional EV engineering methods, we show that our technology improves the efficiency of EV glycoengineering while simplifying and expediting the workflow. Furthermore, we demonstrated the applicability of this technology to EVs derived from the cell lines of different cancer types, including A549, PC3, and COLO-1 cells. Overall, this EV engineering technology could provide a potentially useful tool for broad applications.