Fluid flow is an inherent aspect of solution processing of conjugated polymers. Much of the existing work investigating the effect of flow has been phenomenological, lacking a direct and quantitative connection between the flow gradients and measurable quantities of the conformation or alignment of the conjugated polymers in solution. Furthermore, while aggregation of conjugated polymers in solution has been demonstrated to result in highly aligned thin-films, there are few studies that probe the interplay between the structures that form during aggregation and flow-induced alignment during processing. Here, we explore in detail the influence of flow type, solution aggregation, and concentration on the flow-induced alignment of conjugated polymers. We apply a microfluidic platform to systematically subject the conjugated polymer solution to large and controllable shear and extensional strain rates and use flow-induced retardance (birefringence) measurements to characterize the degree of alignment. By using flow-induced retardance in combination with small angle X-ray scattering (SAXS) and electron microscopy of freeze-dried solutions we are able to determine the solution state structure and clearly demonstrate the interplay between solution aggregation and fluid flow. We determine the overall relaxation time of the material and the strengths of shear and extensional flows required to align conjugated polymer aggregates. Furthermore, we find that although enhanced aggregation can facilitate flow-induced alignment, the type of aggregation and the presence of interparticle interactions at higher concentrations can diminish the effectiveness of flow. The results here demonstrate that there is a complex interplay between the conjugated polymer solution state and fluid flow and that simply increasing the conjugated polymer’s aggregation, concentration, or the strength of flow does not necessarily lead to better or more effective alignment in solution. A careful understanding of the synergy between these two aspects can help to establish design rules in solution processing for improving conjugated polymer film morphology.