A rich in FOS and simple sugar yacon extract was clarified and decoloured and subsequently purified in an activated charcoal column at 25 and 40 °C using two or three stepwise elution with yields of 72.0–86.7% and 90–92.4% purity. Best results were obtained at 25 °C and two stepwise elution, with yield and purity of 81.5% and 92% but 9% sucrose and no glucose and fructose. Different cationic exchange resins on a clarified and demineralised extract at 25 and 60 °C had yields and purity of 73.1–99.4% and 75.0–88.2%, respectively. Best results were obtained with Diaion UBK530Na at 60 °C (99.4% yield and 88.2% purity) but 1.6, 2.7 and 7.5% of fructose, glucose and sucrose. The by-product was rich in sugars (59–60.1% fructose, 28.3–32.8% glucose, 7.2–8.4% sucrose) and could be used by the feed and food industry.