Small Angle Light Scattering (SALS) is employed to determine in-situ microstructural changes of polydisperse colloidal suspensions under capillary flow. Titanium dioxide (rodlike) bundles and kaolinite nano clay (platelet) flake-like stacks of particles are suspended in a Newtonian fluid to explore the effects of shape anisotropy. Subjecting the systems to a startup test in a flow cell in Stokes's regime, the evolution of the anisotropy factor (AF) and the average orientation angle (χ) of particles versus strain is probed at different averaged Péclet ( ) numbers. Dilute and semi-dilute concentration regimes are explored in a capillary flow. Moving in the vorticity direction, we show significant changes in χ due to the gradient in shear rate in the capillary flow, while no cross-sectional flow migration was exhibited. In these polydisperse colloidal suspensions, two characteristic stages are observed, initial particle alignment and subsequent orientational demixing. Probing the velocity-vorticity (xy) plane, an initial particle alignment in the flow direction at high (> 1) occurs, is demonstrated by an elliptical SALS pattern and then an increase in AF is observed due to particles' phase mixing. This behavior is then followed by a breakdown in structure and loss of particle alignment due to orientational demixing. The evolution of the average orientation angle of particles in the xy plane can be clearly observed through these two stages by the help of high-resolution SALS contours. These experimental findings provide novel insights into the flow-microstructure relationship of polydisperse colloidal suspensions for the optimization of many industrial processing schemes.