Fructans and arabinoxylans (AXs) are prebiotics naturally occurring in cereal grains which have well-known beneficial effects on human health. However, the majority of grains consumed by humans are processed prior to the consumption. The effect of baking on fructan and AX levels has been studied in rye breads, but there is a scarcity of data on the presence of fructans and AXs in wheat breads. Therefore, the aim of this study was to investigate the effect of baking on stability of fructans and total AXs in breads made from both wheat and rye flours. Bread loaves were baked using an automatic bread maker Breville BBM100 (Sydney, Australia). Sugar analysis was performed using high-performance liquid chromatography on a Dionex ICS-3000 unit. This study showed slight loss of total AXs (6–10 %) during preparation processes of leavened, yeast-free and unleavened breads. In contrast, there was 40–60 % degradation in fructan content of leavened, but no significant losses of fructans in unleavened breads. Yeast-free breads had higher contents of both fructans and AXs than leavened breads. Generally, smaller changes in the content of these prebiotics were apparent in wholemeal and rye than in white breads. It seems that differences in the structures of AXs and fructans in cereals, and the presence of yeast play significant role in determining stabilities of these components during baking.