AbstractPeruvian carrot and cassava starches were ground in a ball mill for 4, 8, 16, and 32 h and their structural and physicochemical characteristics were determined. Results obtained from HPAEC‐PAD, GPC, and amylose content indicated a breaking of hydrogen bounds and α‐(1 → 6) linkages of the starch molecules after treatment. X‐ray diffractograms showed that the milling provided a reduction in the crystalline area of the starch granules. Most of the starch granules displayed agglomeration after 4 h of milling, when observed under a scanning electron microscope, and after 16 h a shapeless mass was observed for Peruvian carrot starch. Solubility and water absorption capacity of the starches increased with an increase in the milling time, while RVA profiles showed a progressive reduction of peak, breakdown, and final viscosities, as well as the development of initial viscosity. Gelatinization temperatures and enthalpies were reduced. Prolonged ball milling accelerated the enthalpy relaxation in both starches. These results confirmed a partial gelatinization of the starches, which was 82.6% for Peruvian carrot and 65.4% for cassava starches after 32 h of milling. The Peruvian carrot starch was more affected by the ball milling because of both its lower amylose content and the defects in its crystalline structure.