Nutraceuticals and functional foods are increasing in popularity in the recent years. Fructooligosaccharides (FOS) has emerged as functional food ingredient in market and is very well known for its prebiotic properties. Hence, there is a growing need for extensive research on usage and extraction of Fructooligosaccharides. In this study, organic wastes namely onion waste and spoilt wheat have been explored for its potential use in extraction of FOS. The extraction was done using ethanol and optimization was done by considering different initial raw material weights. Thin Layer Chromatography (TLC) confirmed the presence of FOS in the extracts.