A facile continuous production of soy peptide nanogels was demonstrated using a multi-inlet vortex micromixer for the entrapment of active ingredients. The full flow regime in the micromixer was systematically studied to understand the flow impact on nanogel size, drug encapsulation efficiency and drug loading efficiency. Ibuprofen was chosen as a model drug to demonstrate encapsulation capability. The study showed that the nanogel size, drug encapsulation efficiency and drug loading efficiency did not alter significantly as long as the flow rates were in transition and turbulent regimes. The driving force behind the folding of peptides within the microenvironment is kinetic mixing with high flow rates, which dominates in comparison to molecular diffusion, nucleation, and growth. Moreover, the hydrophilic-lipophilic balance of the soy peptides determined the drug encapsulation efficiency and the drug loading efficiency, which did not vary much under different manufacturing parameters. Both characteristics are beneficial to mass production of drug-entrapped peptide. In a 50% water-ethanol mixture, the encapsulation efficiency achieved 70% and the drug loading efficiency was up to 25% in transition and turbulent flow regimes. This work opens the avenues to continuous production of drug-entrapped soy peptide nanogels using a multi-inlet vortex micromixer.