The nanoparticle protein corona alters the biological fate of nanoparticles. Experimental parameters during analysis such as environmental incubation variables alter the rate and extent of nanoparticle-protein interactions. This change is dependent upon the physical and chemical properties of nanoparticles. Here, we examined the role of incubation conditions and variables in model nanoparticle systems. We show that nanoparticles with different surface modifications are differentially susceptible to experimental parameters such as shear flow and incubation duration. Furthermore, we show that the method utilised to isolate particles prior to analysis impact the resulting particle agglomeration and protein corona properties. Our findings demonstrate that careful consideration is needed in the design of sample handling and analysis of nano-bio studies where there is a need to understand nanoparticle behaviour under physiologically relevant conditions.