Yacon, an Andean crop, was historically introduced into Japan for local consumption of its tuberous roots as a sweet vegetable. We recently examined the multi-functional effects of yacon herbal tea to establish the aerial part as a health food material. The current study aimed to investigate whether any functional differences exist among the yacon leaves from four domestic cultivars—‘Sarada otome’ (SY201), ‘Andesu no yuki’ (SY206), ‘Sarada okame’ (SY217), and ‘Andesu no otome’ (SY237)—and a Peru A line (SY11) maintained for several years in the Aso area of Kyushu. The total polyphenol content (TPC) and antioxidant activity of cultivar SY237 exceeded those of SY11, but the values for individual cultivars were inconsistent over the tested years. In carbohydrate-hydrolyzing enzyme inhibition assays, there was a large variation in all cultivars among the tested years, with three cultivars including SY237 partially demonstrating α-glucosidase inhibition comparable to or stronger than that of SY11. Based on multivariate analysis with functional data from over four years, the characteristic positioning of these yacon cultivars was systematically visualized. As a result, we found that SY237 could be a candidate cultivar that is partially superior to SY11, although the yearly variance should be considered.