Bearing multiple functionalities dramatically increases nanomaterial capabilities to enhance analytical assays by improving sensitivity, selectivity, sample preparation, or signal read-out strategies. Magnetic properties are especially desirable for nanoparticles and nanovesicles as they assist in negating diffusion limitations and improving separation capabilities. Here, we propose a microfluidic method that reliably labels functional nanovesicles while avoiding the risk of crosslinking that would lead to large conglomerates as typically observed in bulk reactions. Thus, the carboxy groups of bi-functional biotinylated fluorescent liposomes were activated in bulk. They were then covalently bound to amino group presenting magnetic beads immobilized through a magnetic field within microfluidic channels. Microfluidic design and coupling strategy optimization led to a 62% coupling efficiency when using 1 μm magnetic beads. The yield dropped to 13% with 30 nm magnetic nanoparticles (MNPs) likely due to crowding of the MNPs on the magnet. Finally, both populations of these tri-functional liposomes were applied to a biological binding assay demonstrating their superior performance under the influence of a magnetic field. The microfluidic functionalization strategy lends itself well for massively parallelized production of larger volumes and can be applied to micro- and nanosized vesicles and particles.