Surface modification of nanoparticles is a well‐established methodology to alter their properties to enhance circulation half‐life. While literature studies using conventional, in vitro characterization are routinely used to evaluate the biocompatibility of such modifications, relatively little attention has been paid to assess the stability of such surface modifications in physiologically relevant conditions. Here, microfluidic devices were used to study the effect of factors that adversely impact surface modifications including vascular flow and endothelial cell interactions. Camptothecin nanoparticles coated with polyethylene glycol (PEG) and/or folic acid were analyzed using linear channels and microvascular networks. Detachment of PEG was observed in cell‐free conditions and was attributed to interplay between the flow and method of PEG attachment. The flow and cells also impacted the surface charge of nanoparticles. Presence of endothelial cells further increased PEG shedding. The results demonstrate that endothelial cell contact, and vascular flow parameters modify surface ligands on nanoparticle surfaces.