Cubosomes and hexosomes are emerging platforms for drug and nutraceutical delivery applications. In addition to common high- and low-energy batch emulsification methods for the preparation of these nano-self-assemblies, it is important to introduce suitable microfluidic devices with a precision control of the flow parameters for their continuous production. Microfluidics has several advantages including cost effectiveness, short-production time, and control of the nanoparticle size and size distribution. In the present study, a hydrodynamic flow focusing polyimide microfluidic device was employed for the continuous production of hexosomes based on docosahexaenoic acid monoglyceride (MAG-DHA), in the presence of the stabilizer Pluronic F127. The size, structural, morphological and size characterizations of the continuously produced MAG-DHA nanodispersions were investigated through an integrated approach involving synchrotron small angle X-ray scattering, dynamic light scattering, and cryogenic transmission electron microscopy. We report on a simple process for the microfluidic synthesis of hexosomes with sizes ranging from 108 to 138 nm and relatively narrow size distributions as the polydispersity indices were in the range of 0.14-0.22. At the applied total volumetric flow rates (TFRs) ranging of 50-150 μL min-1 and flow rate ratios (FRRs) of 10-30, it was evident from SAXS findings that ethanol has only a slight effect on the lattice parameter of the internal inverse hexagonal (H2) phase of the produced hexosomes. In addition to hexosomes, cryo-TEM observations indicated the coexistence of vesicular structures and smaller nano-objects. The formation of these nano-objects that are most likely normal micelles was also confirmed by SAXS, particularly on increasing FRR from 10 to 20 or 30 at TFR of 150 μL min-1. Taking into account the reported positive health effects of MAG-DHA, which is a long-chain omega-3 (ω-3) polyunsaturated fatty acid (PUFA) monoglyceride, in various disorders including cancer, the produced hexosomes are attractive for the delivery of ω-3 PUFAs, drugs, nutraceuticals, and their combinations.