Using conventional polymer processing techniques like extrusion, in presence of plasticizers, starch can be converted into a homogenous molten state. Process conditions may lead to different structural changes, or destructuration of starch, such as fragmentation of granules, crystals melting, molecular degradation which have an influence on final material properties. Therefore, a good understanding of starch melting and its rheological behavior is necessary to determine optimal processing conditions and better control of the products quality. That’s why structural changes and starch destructuration have been evaluated depending on extrusion conditions in order to improve current rheological and melting understanding, optimize starch melting using extrusion and minimize material degradation. In this work, two starches of different botanical origin (pea, 33% amylose, and potato, 20% amylose) were processed on a twin-screw extruder under various specific mechanical energy inputs (SME). They were processed in presence of water contents (25, 30, 35%) in order to monitor the melting temperature of starch Tm, determined beforehand by DSC and at temperatures allowing to limit water evaporation and expansion at the die. Starch destructuration was investigated at different structural scales: molecular (chromatography), crystal (X-ray diffraction, DSC), granular (microscopy and paste rheology). Finally, the viscosity of partly molten starch was determined on a pre-shearing rheometer, Rheoplast® (simulating extrusion under controlled conditions). Combined with experimental methods development for destructuration degree evaluation, it enables to suggest interactions mechanisms between rheological behavior, extrusion parameter and transformation degree.