Understanding and engineering the flow-response of complex and non-Newtonian fluids at a molecular level is a key challenge for their practical utilisation. Here we demonstrate the coupling of microfluidics with small angle neutron scattering (SANS). Microdevices with high neutron transmission (up to 98%), low scattering background, broad solvent compatibility and high pressure tolerance (≈3–15 bar) are rapidly prototyped via frontal photo polymerisation. Scattering from single microchannels of widths down to 60 μm, with beam footprint of 500 μm diameter, was successfully obtained in the scattering vector range 0.01–0.3 Å−1, corresponding to real space dimensions. We demonstrate our approach by investigating the molecular re-orientation and alignment underpinning the flow response of two model complex fluids, namely cetyl trimethylammonium chloride/pentanol/D2O and sodium lauryl sulfate/octanol/brine lamellar systems. Finally, we assess the applicability and outlook of microfluidic-SANS for high-throughput and flow processing studies, with emphasis of soft matter.