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The application of nanoparticle in medicine is promising for the treatment of a wide variety of diseases. However, the slow progress in the field has resulted in relatively few therapies being translated into the clinic. Anisotropic synthetic protein nanoparticles (ASPNPs) show potential as a next-generation drug-delivery technology, due to their biocompatibility, biodegradability, and functionality. Even though ASPNPs have the potential to be used in a variety of applications, such as in the treatment of glioblastoma, there is currently no high-throughput technology for the processing of these particles. Insulator-based electrokinetics employ microfluidics devices that rely on electrokinetic principles to manipulate micro- and nanoparticles. These miniaturized devices can selectively trap and enrich nanoparticles based on their material characteristics, and subsequently release them, which allows for particle sorting and processing. In this study, we use insulator-based electrokinetic (EK) microdevices to characterize ASPNPs. We found that anisotropy strongly influences electrokinetic particle behavior by comparing compositionally identical anisotropic and non-anisotropic SPNPs. Additionally, we were able to estimate the empirical electrokinetic equilibrium parameter (e E EEC ) for all SPNPs. This particle-dependent parameter can allow for the design of various separation and purification processes. These results show how promising the insulator-based EK microdevices are for the analysis and purification of clinically relevant SPNPs.