A diet low in fermentable oligo-, di-, monosaccharides and polyols (FODMAPs) is a successful therapeutic approach to alleviate symptoms of irritable bowel syndrome. However, wheat, as a fructan accumulating grain, is a major source of FODMAPs. Baker's yeast degrades fructans during fermentation, yet conventional whole wheat bread is often still high in FODMAPs. In this study, 96 yeast isolates from different environments were screened regarding their capability to metabolise FODMAPs. Two promising isolates were identified: Lachancea fermentati FST 5.1 and Cyberlindnera fabianii NTCyb, and their potential to produce low FODMAP whole wheat bread was compared to baker's yeast (Saccharomyces cerevisiae). A comprehensive characterisation of the carbohydrate metabolism by the different yeasts was achieved via HPAEC-PAD analysis of flour, doughs, and breads. L. fermentati FST 5.1 fermented fructans and excess fructose much more efficiently than baker's yeast and resulted in bread low in FODMAPs (below all cutoff levels known to induce symptoms). In contrast, C. fabianii NTCyb was unable to ferment FODMAPs in the wheat-dough-matrix. Furthermore, the yeasts’ impact on the GC/MS-TOF profile of volatile aroma compounds, the sensory profile, the breads’ ultrastructure, and the technological quality was examined. While C. fabianii NTCyb bread had poor technological and sensory attributes, the quality characteristics (volume, crumb structure, texture, sensory, aroma) of L. fermentati FST 5.1 bread were comparable to the baker's yeast bread. Ultimately, this study identified Lachancea fermentati FST 5.1 as an alternative to baker's yeast to produce low FODMAP whole wheat bread while maintaining optimal bread quality and consumer acceptance.