Yacon (Smallanthus sonchifolius) root is an important source of fructooligosaccharides (FOS). This study evaluated the influence of the blanching and drying processes on the sugars, FOS and colour of the obtained flour. Blanching in boiling water of 5 mm slices for 6 min allowed to inactivate 95% of polyphenol oxidase and peroxidase activity. Blanching solutions containing ascorbic, citric and lactic acid were detrimental in terms of FOS retention (68.2-87.4%) due to hydrolysis mainly of GF3, GF4 and GF5 FOS, and also important losses of reducing sugars (RS) were observed (69.5-87.4% retention). Blanching treatments that included ascorbic acid/CaCl2 prevented RS and FOS losses and improved colour of the obtained flour. The drying tested temperatures of 50-80 °C did not affect the RS retention and FOS losses associated to hydrolysis and the use of 80 °C rapidly reduced the water content and minimised browning reactions yielding flours with excellent colour characteristics with high FOS content that can be derived to the elaboration of prebiotic containing functional foods or for the extraction and purification of FOS.