Salt solubility of pH-shift isolated herring (Clupea harengus) muscle proteins was studied in relation to pH exposure and microstructure using transmission electron microscopy (TEM). Using protein solubilization at pH 11.2 with subsequent precipitation at pH 5.5, salt solubility of the proteins decreased from 78 to 17%. By precipitating the alkali-solubilized proteins at the pH of native herring muscle, 6.5, salt solubility only decreased to 59%, proving that pH values between 6.5 and 5.5 affected protein salt solubility more than the pH cycle 6.5 → 11.2 → 6.5. Precipitation at pH 5.5 resulted in hydrogen bonds, hydrophobic interactions, and S-S bridges, whereas precipitation at pH 6.5 resulted only in the formation of hydrophobic interactions. The alkaline pH-shift isolation process severely rearranged the protein microstructure, with precipitation at pH 6.5 forming a finer, more homogeneous network than precipitation at pH 5.5. The former protein isolate also contained less lipid oxidation products and formed more deformable gels, without affecting protein yield.