Major challenges for optimizing the benefits of fish oil on human health are improved bioavailability while overcoming the strong odor and avoiding significant oxidation of the omega-3 polyunsaturated fatty acids (PUFAs). The scalable continuous flow thin film vortex fluidic device (VFD) improves the Tween 20 encapsulation of fish oil relative to conventional homogenization processing, with the fish oil particles significantly smaller and the content of the valuable omega-3 fatty acids higher. In addition, after 14 days storage the remaining omega-3 fatty acids content was higher, from ca 31.0% for raw fish oil to ca 62.0% of freeze-dried encapsulated fish oil. The VFD mediated encapsulated fish oil was used to enrich the omega-3 fatty acid content of apple juice, as a model water-based food product, without changing its sensory values. The versatility of the VFD was further demonstrated in forming homogenous suspensions of fish oil containing water-insoluble bioactive molecules, curcumin and quercetin. We have also captured, for the first time, real-time structural changes in nanoencapsulation by installing a VFD with in in situ small angle neutron scattering. Real-time measurements afford valuable insights about self-assembly in solution.