Automation is nowadays a preferred way to achieve the efficiency and reproducibility of a chemical process. OnePot is an emerging automated reactor able to ensure reproducibility, scalability, and waste recovery due to its innovative heating technology and sensor system. In this investigation, we demonstrate its applicability to the scaling-up of polymeric nanoparticles. Natural proteins such as zein have emerged as promising raw materials for the development of nanoparticles due to their biocompatibility, safety, and biodegradability. The physicochemical properties and stability of zein-based nanoparticles prepared using different methods, including the innovative OnePot approach, were investigated. The nanoparticles showed mean sizes ranging from ∼130 to 160 nm, a narrow size distribution, and a positive zeta-potential (15 mV). Despite the considerable volume, the OnePot-assisted method demonstrated robustness and efficiency in realizing stable nanoparticles without compromising their physicochemical properties. The evaluation of in vitro toxicity performed on MCF-7 and CaCo-2 cell lines demonstrated no significant differences between the standard nanoprecipitation method and the OnePot-assisted approach. Both formulations were characterized by notable cytotoxicity only at a concentration of 250 μg/mL protein. The comparative analysis showed that the OnePot-assisted method offers substantial time and energy savings compared to conventional procedures, promoting a significant decrease in energy consumption. These findings demonstrated the suitability of the OnePot-assisted method in the development of large amounts of stable zein nanoparticles and also provided evidence of its potential positive impact in the scale-up of various colloidal formulations.