Starches were extracted from three varieties of native Andean potatoes (Solanum tuberosum var amarilla, Solanum tuberosum sbsp. Andigena var huamantanga, and Solanum tuberosum sbsp. Andigena var tomasa). Starch-based nanocomposite films were prepared using starch as the matrix and starch nanoparticles as the reinforcement at 3, 5, and 7 wt%. The mechanical properties of the prepared nanocomposites were assessed by tensile tests. The results show that the mechanical properties of the nanocomposite films vary depending on both the amount of reinforcement present, and the botanical origin of the starch. In addition, the highest increases of elastic moduli (up to 1.5–3 times) are found when a film's matrix and reinforcement nanoparticles are prepared from a single botanical source.