The blood-brain barrier (BBB) maintains the homeostasis of the central nervous system, which is one of the reasons for the treatments of brain disorders being challenging in nature. Nanoparticles (NPs) have been seen as potential drug delivery systems to the brain overcoming the tight barrier of endothelial cells. Using a BBB model system based on human induced pluripotent stem cells (iPSCs), the impact of polymeric nanoparticles has been studied in relation to nanoparticle size, material, and protein corona. PLGA [poly(lactic-co-glycolic acid)] and PLLA [poly(d,l-lactide)] nanoparticles stabilized with Tween® 80 were synthesized (50 and 100 nm). iPSCs were differentiated into human brain microvascular endothelial cells (hBMECs), which express prominent BBB features, and a tight barrier was established with a high transendothelial electrical resistance of up to 4000 Ω cm2. The selective adsorption of proteins on the PLGA and PLLA nanoparticles resulted in a high percentage of apolipoproteins and complement components. In contrast to the prominently used BBB models based on animal or human cell lines, the present study demonstrates that the iPSC-based model is suited to study interactions with nanoparticles in correlation with their material, size, and protein corona composition. Furthermore, asymmetrical flow field-flow fractionation enables the investigation of size and agglomeration state of NPs in biological relevant media. Even though a similar composition of the protein corona has been detected on NP surfaces by mass spectrometry, and even though similar amounts of NP are interacting with hBMECs, 100 nm-sized PLGA NPs do impact the barrier, forming endothelial cells in an undiscovered manner.