Functionalized electrospun nanofibers were integrated into microfluidic channels to serve as on-chip bioseparators. Specifically, poly(vinyl alcohol) (PVA) nanofiber mats were shown to successfully serve as bioseparators for negatively charged nanoparticles. Nanofibers were electrospun onto gold microelectrodes, which were incorporated into poly(methyl methacrylate) (PMMA) microfluidic devices using UV-assisted thermal bonding. PVA nanofibers functionalized with poly(hexadimethrine bromide) (polybrene) were positively charged and successfully filtered negatively charged liposomes out of a buffer solution, while negatively charged nanofibers functionalized with Poly(methyl vinyl ether-alt-maleic anhydride) (POLY(MVE/MA)) were shown to repel the liposomes. The effect of fiber mat thickness was studied using confocal fluorescence microscopy, determining a quite broad optimal range of thicknesses for specific liposome retention, which simplifies fiber mat production with respect to retention reliability. Finally, it was demonstrated that liposomes bound to positively charged nanofibers could be selectively released using a 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)-sucrose-saline (HSS) solution of pH 9, which dramatically changes the nanofiber zeta potential and renders the positively charged nanofibers negatively charged. This is the first demonstration of functional electrospun nanofibers used to enable sample preparation procedures of isolation and concentration in lab-on-a-chip devices. This has far reaching impact on the ability to integrate functional surfaces and materials into microfluidic devices and to significantly expand their ability toward simple lab-on-a-chip devices.