Andean tubers and tuberous roots have nutritional and medicinal properties transferred through ancestral generations. In this study, we aim to promote cultivation and consumption by developing a snack based on these crops. Corn grits were thoroughly mixed with sweet potato, mashua, and three varieties of oca flour (white, yellow, and red) in an 80:20 ratio, and a single-screw laboratory extruder was utilized to produce third-generation (3G) dried pellets. Microwave expansion was studied, and the dried 3G pellets and expanded snacks were characterized. The microwave expansion curves of the dried 3G pellets were adjusted to the Page, logarithmic, and Midilli–Kucuk models. During the characterization, the influence of the raw material composition was observed in sectional expansion, water content, water activity, water absorption, water solubility, swelling, optical and textural properties, and bioactive compounds. According to global color variation (mixture vs. expanded and dried vs. expanded) and bioactive compound analysis, the mashua suffered little chemical change or nutritional loss during the process. The extrusion process was shown to be an ideal method for manufacturing snacks from Andean tuber flours.