Arracacha (Arracacia xanthorrhiza Bancroft) is an underexplored Andean root with a high starch content. In this work, starches from two different varieties of Peruvian arracacha were evaluated and characterized in relation to their granule morphology, molecular structure and properties. The starches presented round or polygonal shapes, with a mean diameter of ~20 μm and B-type granules. They were rich in amylopectin molecules with long chain lengths (with the ability to complex iodine) and some with intermediate sizes (indicating a defective crystalline structure). The starches presented low gelatinization temperature, enthalpy of gelatinization and tendency to retrogradation and high peak apparent viscosity and swelling capacity, even at moderate temperatures (60 °C), characteristics of high interest for industrial purposes. Besides, the starches presented a smooth and elastic gel and a high paste clarity. Overall, the arracacha roots presented attractive properties and can be used as an alternative botanical source for starch extraction.