Onion soluble non-structural carbohydrates consist of fructose, glucose and sucrose plus fructooligosaccharides (FOS) with degrees of polymerisation (DP) in the range of 3-19. In onion, sugars and FOS are typically separated using liquid chromatography (LC) with acetonitrile (ACN) as a mobile phase. In recent times, however, the production of ACN has diminished due, in part, to the current worldwide economic recession. A study was therefore undertaken, to find an alternative LC method to quantify sugars and FOS from onion without the need for ACN. Two mobile phases were compared; the first taken from a paper by Vågen and Slimestad (2008) using ACN mobile phase, the second, a newly reported method using ethanol (EtOH). The EtOH mobile phase eluted similar concentrations of all FOS compared to the ACN mobile phase. In addition, limit of detection, limit of quantification and relative standard deviation values were sufficiently and consistently lower for all FOS using the EtOH mobile phase. The drawback of the EtOH mobile phase was mainly the inability to separate all individual sugar peaks, yet FOS could be successfully separated. However, using the same onion extract, a previously established LC method based on an isocratic water mobile phase could be used in a second run to separate sugars. Although the ACN mobile phase method is more convenient, in the current economic climate a method based on inexpensive and plentiful ethanol is a valid alternative and could potentially be applied to other fresh produce types. In addition to the mobile phase solvent, the effect of extraction solvents on sugar and FOS concentration was also investigated. EtOH is still widely used to extract sugars from onion although previous literature has concluded that MeOH is a superior solvent. For this reason, an EtOH-based extraction method was compared with a MeOH-based method to extract both sugars and FOS. The MeOH-based extraction method was more efficacious at extracting sugars and FOS from onion flesh, eluting significantly higher concentrations of glucose, kestose, nystose and DP5-DP8.