We report the differences in nanoparticle protein corona impact on the physical and characteristics of nanoparticles in response to different experimental protocols used for the isolation of nanoparticles prior to analysis. With most nanoparticles intended for parenteral administration it becomes crucial to understand the impact of physiological shear flow conditions on nanoparticle-protein interactions and subsequent protein corona formation. Here, we investigate the impact of existing nanoparticle recovery approaches and shear flow conditions on nanoparticle parameters following exposure to protein containing media. To our knowledge, while extensive evaluation of the protein corona composition has been performed in nanoparticles to-date, the impact of co-incubation with protein has been investigated to a lesser extent.