Dehulled yellow pea flour (48.2% starch, 23.4% proteins, d.b.), was processed by a twin-screw extruder at various moisture contents MC (18–35% w.b.), product temperature T (115–165 °C), and specific mechanical energy SME (50–1200 kJ/kg). Structural changes of extruded pea flour were determined at different scales by measurements of density (expansion), crystallinity (X-ray diffraction), gelatinisation enthalpy (DSC), starch solubility in water and protein solubility in SDS and DTE (SE-HPLC). Foam density dropped from 820 to 85 kg/m3 with increase in SME and T (R2 ≥ 0.78). DSC and XRD results showed that starch was amorphous whatever extrusion conditions. Its solubility in water augmented up to 50%. Increasing temperature from 115 to 165 °C decreased proteins soluble in SDS from 95 to 35% (R2 = 0.83) of total proteins, whereas the proteins soluble in DTE increased from 5 to 45% (R2 = 0.75) of total proteins. These trends could be described by sigmoid models, which allowed determining onset temperatures for changes of protein solubility in the interval [125, 146 °C], whatever moisture content. The SME impact on protein solubility followed similar trends. These results suggest the creation of protein network by Ssingle bondS bonds, implicating larger SDS-insoluble protein aggregates, as a result of increasing T and SME, accompanied by creation of covalent bonds other than Ssingle bondS ones. CSLM images suggested that extruded pea flour had a composite morphology that changed from dispersed small protein aggregates to a bi-continuous matrix of large protein aggregates and amorphous starch. This morphology would govern the expansion of pea flour by extrusion.