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Rice pellets were produced by extrusion according to an experimental design varying temperature (120–135–150 °C), moisture content (17–20–23%) and screw speed (300–400–500 rpm). The internal expanded structure of the pellets was assessed by X-ray tomography and texture with a texture analyser. The extent of starch depolymerisation and the types of protein depolymerisation/interactions were studied in complement to the starch–proteins morphology assessed by microscopy. The physico-chemical properties of the pellets were mainly affected by moisture and temperature, with moisture having the highest impact. High moisture content (23%) resulted in higher mean walls thickness of the extruded pellet, less starch depolymerisation, more protein aggregation through disulfide bonds and harder pellets. The internal expanded structure and texture of the rice pellets were mainly explained by protein changes and less by the extent of starch depolymerisation in this study. When proteins mainly interacted through medium energy interactions (disulfide bonds), protein aggregates were larger, cells walls thicker and pellets were less porous and harder with more fracture events. On the contrary, when proteins interacted through low energy (hydrogen and hydrophobic bonds) and high energy bonds (unextractable proteins), proteins were more depolymerised and aggregates were smaller and finely distributed, cells walls thinner and pellets were less hard with less fracture events.