High-moisture extrusion (HME) is a proven industrial food processing technique used to create textured plant-protein materials that can serve as alternatives for animal meat. The required multiscale anisotropic structure of the extrudate can be achieved by selecting suitable HME process conditions, as well as by pH-shifting. In this work, we explored pH-shifting via the water feed, which is an attractive industrially-scalable approach. Soy protein concentrate (SPC) was extruded on lab-scale and extrudates were characterized ex situ, from molecular to mm scale, using Diffuse Reflectance (DR), Magnetic Resonance Imaging (MRI), Small-Angle-Scattering of Neutrons (SANS) or X-rays (SAXS). pH-shifting had a non-monotonic effect on extrudate hardness and anisotropic structure at both sub-mm (MRI) and μm (DR) scale. At the sub-μm scale, SANS and SAXS data indicated that, at pH > pI, the radius of protein nano-aggregates monotonically increases, accompanied by a transition from particulate to fibrillar protein aggregation. When pH was further shifted to alkaline conditions, the decrease in clustering strength and nematic order parameter pointed to an increase in intra- and inter-fibrillar repulsion, respectively. Protein extractability experiments indicated that the effects of pH-shifting on anisotropic structure formation could not be attributed to covalent intermolecular crosslinking. Thus, repulsive non-covalent electrostatic protein-protein interactions play a dominant role in the formation of multiscale anisotropic structure during SPC extrusion. The formation of an optimal anisotropic SPC extrudate structure is determined by the pH-dependent balance between fibrillar nano-aggregate clustering and electrostatic repulsion. Alkalization or acidification via the water feed implies that protein charge and structure may not be in equilibrium yet with the imposed pH conditions. The transient nature of pH-shifting via the water feed results in an intricate interplay with extrusion conditions. Therefore, control of anisotropic structure formation, via the water feed, in SPC extrudates, is extruder specific.