This research aimed to characterize the physicochemical, in vitro digestion, and structural features of digestion residues of maize and sorghum starches subjected to thermoplastic extrusion, along with the influence of Sodium Stearoyl Lactylate (SSL), to obtain improved starches for food applications and to understand their behavior when consumed as a food ingredient. The morphology of the extruded materials showed remanent starch granules when SSL was used. A higher amount of medium and large linear glucan chains were found in these particles, influencing higher thermal stability (ΔH ≈ 4 J/g) and a residual crystallinity arrangement varying from 7 to 17% in the extrudates. Such structural features were correlated with their digestibility, where slowly digestible starch (SDS) and resistant starch (RS) fractions ranged widely (from 18.28 to 27.88% and from 0.13 to 21.41%, respectively). By analyzing the data with a Principal component analysis (PCA), we found strong influences of B2 and B3 type chains on the thermal stability of the extrudates. The amylose and smaller glucan chains (A and B1) also significantly affected the emulsifying and foam stability properties. This research contributes to the molecular knowledge of starch in extruded products with broad food applications.