Acid- and pepsin-induced milk protein coagulation plays a crucial role in the gastric digestion of milk. Real-time structural evolution at a nano- (e.g. colloidal calcium phosphate (CCP) and micelle) and micro- (gel network) level of unheated and heated (85 °C for 30 min) bovine milk was examined under acidic conditions and at low and high concentrations of pepsin using ultra-small- and small-angle neutron scattering (USANS and SANS), small-amplitude oscillatory rheometry and confocal scanning laser microscopy. Milk was treated with glucono-δ-lactone (GDL), pepsin or a combination of GDL and pepsin to induce coagulation. Heat-treated milk showed a faster increase in elastic storage modulus (G′) and scattering intensity (USANS and SANS) compared with unheated milk when coagulated with GDL or the combination of GDL and pepsin. At pH 6.3, heat treatment retarded pepsin (1.10 U/mL)-induced milk coagulation, with slower increases in G′ and scattering intensity. At a high concentration of pepsin (2000 U/mL) that mimics the concentration found in the stomach, general proteolysis followed coagulation. Heat treatment retarded coagulation but accelerated curd proteolysis. This study demonstrates how time-resolved USANS and SANS can be used to investigate the structural evolution of protein coagulation and degradation under gastric environment conditions at nano- and micro-metre length scales.