Cassava (Manihot esculenta) is an important tropical crop and a valuable source of starch for food processing. This study evaluated the effect of three cassava ecotypes from Cajamarca, Peru-Puerto Huallape (PHE), Las Naranjas (LNE), and Puerto Chinchipe (PCE), on the quality and technological properties of naturally fermented sour cassava starch. Native starches were subjected to spontaneous fermentation followed by solar drying, and their fermentation kinetics, physicochemical, thermal, functional, and pasting properties were evaluated. The ecotypes required 4 to 5 days of fermentation to reach the target acidity and pH, followed by approximately 7 h of solar drying. Significant differences (p < 0.05) were observed among ecotypes in yield, pH, titratable acidity, moisture, water activity, whiteness index, expansion capacity, water absorption and solubility indices, gelatinization parameters and pasting properties. PHE exhibited the highest expansion capacity and peak viscosity, indicating greater potential for bakery applications; LNE showed the highest water absorption index, greater paste stability, and stronger molecular reassociation during cooling, whereas PCE exhibited greater fermentation intensity and a higher gelatinization temperature. Principal component analysis identified expansion capacity, whiteness, moisture, and water activity as the main variables differentiating the ecotypes. Furthermore, the results demonstrate significant differences among sour cassava starches obtained from three Peruvian ecotypes via natural fermentation and sun drying, allowing for their physicochemical differentiation; this provides a basis for selecting raw materials according to specific technological requirements, particularly for gluten-free baking applications.