The aim of this study was to evaluate the quality characteristics of seven yacon (Smallanthus sonchifolius Poepp. and Endl.) cultivars (Cajamarca, Cusco, Early White, Late Red, Morado, New Zealand and Quinault) cultivated in the southwest of Germany. The following phyto/chemical traits were investigated in different yacon tuber parts (flesh, peel, and whole tubers): total dry matter, sugar content (fructose, glucose, and sucrose content), total phenolic content (TPC), total flavonoid content (TFC), 2,20-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activity, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, and Ferric reducing antioxidant power (FRAP). The results indicated a significant interaction between cultivar and tuber part on all of the examined traits (p < 0.0001). Of flesh and whole tuber, cv. Late Red, cv. Morado, and cv. Cajamarca had the highest TPC, TFC, DPPH radical scavenging activity, and FRAP. They also had relatively higher total sugar content. Cv. New Zealand had the lowest amount of sugars, TPC, TFC, DPPH radical scavenging activity, and FRAP, but the highest ABTS radical scavenging activity content in its flesh and whole tuber. Moreover, the results indicated that the peel of yacon tubers contained considerably high amounts of phytochemicals while possessing low sugar contents. Overall, this study provides a broad insight into the phyto/chemical content of yacon tubers from different cultivars, which can be used for further breeding programs, and the selection of proper cultivars for specific food product development.