Microreactors have been shown to be a powerful tool for the production of nanoparticles (NPs); however, there is still a lack of understanding of the role that the microfluidic environment plays in directing the nanoprecipitation process. Here we investigate the mechanism of nanoprecipitation of block copolymer stabilized organic NPs using a microfluidic-based reactor in combination with computational fluid dynamics (CFD) modelling of the microfluidic implementation. The latter also accounts for the complex interplay between molecular and hydrodynamic phenomena during the nanoprecipitation process, in order to understand the hydrodynamics and its influence on the NP formation process. It is demonstrated that the competitive reactions result in the formation of two types of NPs, i.e., either with or without loading organic actives. The obtained results are interpreted by taking into consideration a new parameter representing the mismatching between the aggregations of the polymers and actives, which plays a decisive role in determining the size and polydispersity of the prepared hybrid NPs. These results expand the current understanding of the co-nanoprecipitation mechanism of active and block copolymer stabilizer, and on the role exerted by the microfluidic environment, giving information that could be translated to the emerging fields of microfluidic formation of NPs and nanomedicine.