Sourdough fermentation has been shown to have numerous beneficial effects on bread quality, and nutritionally enhance soy‐supplemented bread by altering isoflavone chemical forms. Given this, the objective of this study was to compare the loaf quality and shelf life of sourdough and yeast‐leavened soy breads by various physical, thermal, and sensorial methods, and to assess the effects of fermentation by various microorganisms on isoflavone profile in dough and breads using high‐performance liquid chromatography analysis. Sourdough fermentation yielded a less extensible dough compared to yeast‐leavened soy dough (P < 0.001), and resulted in a harder bread crumb (P < 0.05) and lighter crust color (P < 0.001), compared to yeast‐leavened soy bread (Y‐B). Sensory analysis revealed a significantly higher overall liking of Y‐B compared to sourdough soy bread (SD‐B) (P < 0.001). Segmentation analysis of the cohort suggests that overall liking and bread consumption frequency may be determinants of Y‐B or SD‐B preference. SD‐B and Y‐B exhibited similar shelf‐life properties. Despite significantly different enthalpies associated with the melting of amylose‐lipid complexes, thermal analysis of the 2 soy breads stored for 10 d (ambient conditions) demonstrated no significant difference in water distribution and starch retrogradation (P < 0.05). Lastly, SD‐B was determined to have 32% of total isoflavones occurring in the aglycone form compared to 17% in Y‐B. These findings warrant further investigation of sourdough fermentation as a processing technique for quality and nutritional enhancement of soy‐based baked goods.