We investigate the effect of microfluidic flow on the microstructure and dynamics of a model surfactant mixture, combining synchrotron Small Angle X-ray Scattering (SAXS), microscopy and rheology. A system comprising a single-chain cationic surfactant, hexadecyl trimethyl ammonium chloride (C16TAC), a short-chain alcohol (1-pentanol) and water was selected for the study due to its flow responsiveness and industrial relevance. Model flow fields, including sequential contraction-expansion (extensional) and rotational flows, were investigated and the fluid response in terms of the lamellar d-spacing, orientation and birefringence was monitored in situ, as well as the recovery processes after cessation of flow. Extensional flows are found to result in considerable d-spacing increase (from approx 59 Å to 65 Å). However, under continuous flow, swelling decreases with increasing flow velocity, eventually approaching the equilibrium values at velocities ≃2 cm s(-1). Through individual constrictions we observe the alignment of lamellae along the flow velocity, accompanied by increasing birefringence, followed by an orientation flip whereby lamellae exit perpendicularly to the flow direction. The resulting microstructures are mapped quantitatively onto the flow field in 2D with 200 µm spatial resolution. Rotational flows alone do not result in appreciable changes in lamellar spacing and flow type and magnitude evidently impact the fluid microstructure under flow, as well as upon relaxation. The findings are correlated with rheological properties measured ex situ to provide a mechanistic understanding of the effect of flow imposed by tubular processing units in the phase behavior and performance of a model surfactant system with ubiquitous applications in personal care and coating industries.