The root contain an indigestible sugar, which means that although they have a sweet flavor, the roots contain fewer calories than would be expected. To put this in simple words, the specific sugar contained in the Yacon roots is not influencing the blood sugar level, hence its potential use for diabetics and in body weight control.

The undigested portion of Yacon serves as food for "friendly" bacteria, such as bifidobacterium and Lactobacillus species, in the colon. Clinical studies have shown that administering FOS can increase the number of these friendly bacteria in the colon while simultaneously reducing the population of harmful bacteria.