Collagen is a major component of the extracellular matrix that exhibits unique hierarchical organization at multiple length scales ranging from nano to macroscale. Despite numerous methods to create collagen-based biomaterials, the self-assembly process of collagen ex vivo is poorly understood. Here, we describe a system that uses a microfluidic method to investigate the dynamics of collagen self-assembly. A main inlet stream of semidilute soluble collagen-I is hydrodynamically focused by two side inlet streams, which gradually increases the pH in the main stream. This enables dynamic nonequilibrium investigation of the self-assembly process simultaneously at different positions and therefore different stages in the assembly process within the same system. The device is designed for in situ monitoring and characterization of collagen assembly using polarization microscopy and X-ray diffraction: the continuous extensional flow provides highly ordered phases of the macromolecules over a large distance in the outlet microchannel and allows for data collection without material damage. We further demonstrate that finite element method simulations provide a good description of our experimental results regarding the diffusive phenomena, flow profile, and pH distribution. Our approach has broad impact, since it provides a powerful means of controlling and investigating the dynamic self-assembly process of biomacromolecules.