Bioinspired materials have been developed with the aim of harnessing natural self-assembly for precisely engineered functionality. Microfluidics is poised to play a key role in the directed assembly of advanced materials with ordered nano and mesoscale features. More importantly, there is a strong need for understanding the kinetics of continuous assembly processes. In this work, we describe a continuous microfluidic system for the assembly and alignment of synthetic oligopeptides with π-conjugated cores using a three-dimensional (3D) flow focusing of inlet reactant streams. This system facilitates in situ confocal fluorescence microscopy and in situ fluorescence lifetime imaging microscopy (FLIM), which can be used in unprecedented capacity to characterize the integrity of peptides during the assembly process. To achieve continuous assembly, we integrate chevron patterns in the ceiling and floor of the microdevice to generate a 3D-focused sheath flow of the reactant peptide. Consequently, the peptide stream is directed toward an acidic triggering stream in a cross-slot geometry which mediates assembly into higher-order fiber-like structures. Using this approach, the focused peptide stream is assembled using a planar extensional flow, which ensures high degrees of microstructural alignment within the assembled material. We demonstrate the efficacy of this approach using three different synthetic oligopeptides, and in all cases, we observe the efficient and continuous assembly of oligopeptides. In addition, finite element simulations are used to guide device design and to validate 3D focusing. Overall, this approach presents an efficient and effective method for the continuous assembly and alignment of ordered materials using microfluidics.