Fermentable oligo-, di-, and monosaccharides and polyols (FODMAPs) are associated with digestive disorders and with diseases such as irritable bowel syndrome. In this study, we determined the FODMAP contents of bread, bakery products, and flour and assessed the effectiveness of sourdough fermentation for FODMAP reduction. The fermentation products were analyzed to determine the DP 2–7 and DP >7 fructooligosaccharide (FOS) content of rye and wheat sourdoughs. FOSs were reduced by Acetobacter cerevisiae, Acetobacter okinawensis, Fructilactobacillus sanfranciscensis, and Leuconostoc citreum to levels below those in rye (−81%; −97%) and wheat (−90%; −76%) flours. The fermentation temperature influenced the sourdough acetic acid to lactic acid ratios (4:1 at 4 °C; 1:1 at 10 °C). The rye sourdough contained high levels of beneficial arabinose (28.92 g/kg) and mannitol (20.82 g/kg). Our study contributes in-depth knowledge of low-temperature sourdough fermentation in terms of effective FODMAP reduction and concurrent production of desirable fermentation byproducts.