Silk has a long track record of clinical use in the human body, and new formulations, including silk nanoparticles, continue to reveal the promise of this natural biopolymer for healthcare applications. Native silk fibroin can be isolated directly from the silk gland, but generating sufficient material for routine studies is difficult. Consequently, silk fibroin, typically extracted from cocoons, serves as the source for nanoparticle formation. This silk requires extensive processing (e.g., degumming, dissolution, etc.) to yield a hypoallergenic aqueous silk stock, but the impact of processing on nanoparticle production and characteristics is largely unknown. Here, manual and microfluidic-assisted silk nanoparticle manufacturing from 60- and 90-min degummed silk yielded consistent particle sizes (100.9-114.1 nm) with low polydispersity. However, the zeta potential was significantly lower ( < 0.05) for microfluidic-manufactured nanoparticles (-28 to -29 mV) than for manually produced nanoparticles (-39 to -43 mV). Molecular weight analysis showed a nanoparticle composition similar to that of the silk fibroin starting stock. Reducing the molecular weight of silk fibroin reduced the particle size for degumming times ≤30 min, whereas increasing the molecular weight polydispersity improved the nanoparticle homogeneity. Prolonged degumming (>30 min) had no significant effect on particle attributes. Overall, the results showed that silk fibroin processing directly impacts nanoparticle characteristics.