Amylose is well known to be organized helically with six glucose per turn, allowing it to form complexes with various ligands. This interaction can be affected by the type of crystalline structure present in the starch sources. This study evaluated the effect of extrusion on the crystalline structure of starch during RS5 formation. Rice and potato starches were extruded at 100 °C and 15 rpm with 5% and 10% oleic acid (OA), then the physical, thermal, paste properties, and resistant starch content (RS) were evaluated. Potato starch extruded with 10% OA showed granules embedded in a gelatinized starch matrix. The X-ray revealed that rice (orthorhombic) and potato (hexagonal) structures remain unchanged even after extrusion. Differential scanning calorimetry (DSC) evidenced the formation of type IIa amylose-lipid complexes in OA treatments, where potato extruded with 10% OA had the highest enthalpy (0.9 J/g). Moreover, the extruded potato showed the highest pasting temperature (87.19 °C), supporting the complex formation. The RS was reduced from 15.8 (isolated) to 4.14 mg/100 mg (extruded 10% OA) in rice. For potato, RS decreased from 17 to 13 mg/100 mg (isolated and extruded 10% OA). Overall, these findings suggest a tendency in potato starch (ortho-rhombic) to interact with OA during the extrusion process, promoting a crystalline lamellae growth when extruded with 10% OA; therefore, changing their properties.