Marine mussels fabricate tough collagenous fibers known as byssal threads to anchor themselves. Threads are produced individually in minutes via secretion of liquid crystalline (LC) collagenous precursors (preCols); yet the physical and chemical parameters influencing thread formation remain unclear. Here, we characterized the structural anisotropy of native and artificially induced threads using quantitative polarized light microscopy and transmission electron microscopy to elucidate spontaneous vs regulated aspects of thread assembly, discovering that preCol LC phases form aligned domains of several hundred microns, but not the cm-level alignment of native threads. We then explored the hypothesized roles of mechanical shear, pH, and metal ions on thread formation through in vitro assembly studies employing a microfluidic flow focusing device using purified preCol secretory vesicles. Our results provide clear evidence for the role of all three parameters in modulating the structure and properties of the final product with relevance for fabrication of collagenous scaffolds for tissue engineering applications.