Three cultivars of bitter potatoes (Cuchi jipilla, Ocucuri negra, and Pala), grown in the Andean region of Peru (3862 m above sea level), and their “Tuntas” were used for starch isolation. “Tunta” is obtained from the natural freeze-thaw (F/T) treatment of these bitter potatoes. The structural, functional, and rheological characteristics of starches from bitter potatoes (PS) and their “Tuntas” (TS) were determined to evaluate the effect of F/T treatment. Among the results, TS showed lower apparent amylose content, lower gelatinization enthalpies, and higher syneresis values in refrigeration than PS. Scanning electron microscope (SEM) micrographs did not exhibit differences on PS and TS granules surfaces. The mean size D[4,3] of the starch granules from bitter potatoes and “Tuntas” ranged between 36.3 and 43.1 μm. FT-IR analysis showed that the chemical structure of starch granules from “Tunta” was not significantly affected by the natural F/T treatment. Pasting profiles of PS exhibited higher properties than TS. All starch gels showed a pseudoplastic behavior (0.48 ≤ η ≤ 0.53) which the Herschel-Bulkley model well described. In addition, PS and TS gels showed an elastic behavior (G’ > G’’). The results suggest that PS and TS exhibited significant differences in their structural, functional, and rheological characteristics, which make them feasible for food and non-food applications.