Starch is among the biopolymers that have been successfully used to extract nanoparticles through a variety of processing routes. Most of these processes require chemical or mechanical-physical treatments that erode and break down the starch granules into nanoparticles. We have evaluated the use of four treatments for the production of starch-based nanoparticles from three varieties of native Andean potatoes. These treatments include either an acid or alkaline hydrolysis stage to disrupt the starch granules’ structure. We have assessed the morphology and size of these nanoparticles. It is found that, in the case of acid-based treatments, the size of the nanoparticles is dependent on the variety of potato used. In the case of the alkali-based treatments, the sizes obtained are statistically independent of the variety of potato used. In addition, the acid-based treatments are found to preserve the crystalline structure of the variety of starch used whereas the alkali-based treatments destroy the starch granules and change the crystalline structure of the starch. Different processing routes can be used to customize the specific properties of starch nanoparticles. The results suggest that native starch sources can be used to obtain starch nanoparticles with tailor-made properties.