Moringa oleifera (M. oleifera) is globally recognized for its medicinal properties and offers high-quality, protein-rich seeds. This study aimed to explore the potential of M. oleifera seeds as a significant source of protein-based nanoparticles (PBNPs) using the ultrasonication technique after desolvation and to evaluate their cytotoxicity in the human leukemia cell line (THP-1) for the first time. The properties of the PBNPs were confirmed by dynamic light scattering (DLS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FT-IR). The extracted protein from moringa seed cake flour had a significant protein content of 54.20%, and the resulting PBNPs had an average size of 134.3 ± 0.47 nm with a robust zeta potential of −43.15 mV. Notably, our study revealed that PBNPs exhibited cytotoxic potential at high concentrations, especially against the THP-1 human leukemia cell line, which is widely used to study immunomodulatory properties. The inhibitory effect of PBNPs was quantitatively evidenced by a cytotoxicity assay, which showed that a concentration of 206.5 μg mL−1 (log conc. 2.315) was required to inhibit 50% of biological activity. In conclusion, our findings highlight the potential of M. oleifera seeds as a valuable resource in the innovative field of eco-friendly PBNPs by combining traditional medicinal applications with contemporary advancements in protein nanotechnology. However, further studies are required to ensure their biocompatibility.