The composition of soluble carbohydrates such as fructooligosaccharides (FOS) in onions ( Allium cepa L.) plays a role regarding their digestibility, long-term storability, and processability. Qualitative and quantitative profiles of soluble carbohydrates were determined in 23 different onion samples comprising 20 cultivars grown at two different locations in 2014 and 2015. FOS concentrations were 1.1-fold higher in set grown onions than in seed grown onions ( p = 0.001). FOS levels of dehydrator cultivars were higher (overall average: 130.8 ± 42.4 g/L FOS) than those of common set and seed (61.8 ± 20.0 and 29.4 ± 14.7 g/L FOS) grown cultivars. Consequently, cultivation method (seed vs. set planting) and cultivar selection were crucial when aiming at onions with defined FOS contents. Besides FOS and other carbohydrate-related parameters, levels of alk(en)yl cysteine sulfoxides, indicating onion oil yield and pungency of onions, were determined to be different in dehydrator onions (13.1 ± 2.6 μmol/mL), seed (8.4 ± 1.3 μmol/mL), and set grown onions (7.5 ± 1.6 μmol/mL).