The development of novel plant-based meat alternatives that closely mimic the anisotropic structure of animal meat offers a solution to mitigate the adverse effects of animal meat consumption. The currently most widely adopted production route is shear processing through high-moisture extrusion (HME). The complex structure formation mechanisms that determine the final fibrous texture of extrudates have yet to be fully understood. The main obstacle is the lack of multiscale studies investigating the principles governing structure formation from the nano- to the macro-structural level. This work aims to address this knowledge gap by studying materials, collected after a dead-stop operation of an industrial pilot-plant scale extruder, with multiple characterisation techniques, such as Magnetic Resonance Imaging (MRI) and Small-Angle Scattering (SAS). We demonstrate that the nm- to μm-scale structure is formed already within the extruder barrels, and that sub-mm-scale anisotropy develops within the cooling die. Furthermore, we show that diffuse light reflectance (DR) probes the size and coarseness of the lamellar phase-separated regions.