Wheat sourdough is a common traditional fermented food that is produced worldwide. However, product quality of spontaneous sourdough is not easy to control because it depends on natural fermentation and backslopping, about which little is known, notably after ten backslopping steps. To this end, we tracked the spontaneous fermentation of three sourdoughs made from wheat flours during 32 backslopping steps for 60 days. At 24 time points, the microbial community was analyzed by both culture-dependent and culture-independent methods and its chemical constituents were assessed. Dynamic changes were observed in the microbial community, which showed a common succession pattern among the three sourdoughs at the bacterial family level and differences at the species level. The bacterial communities evolved through three phases that were driven by different groups of lactic acid bacteria (LAB) species. The dynamism among the metabolites also differed, depending on the species composition of the LAB and yeast communities. In one sourdough, the growth of Saccharomyces cerevisiae was detected along with a concentration of increased ethanol, while in the other two sourdoughs, Wickerhamomyces anomalus was detected without ethanol production. Regarding the LAB communities, two sourdoughs were eventually co-dominated by Lactobacillus plantarum and L. brevis, while the other sourdough was eventually dominated solely by the heterolactic fermentative bacterium Lactobacillus fermentum, and ethanol was produced at the same level as lactic acid. Further research is needed to determine the bacterial and yeast species involved in the fermentation of sourdough, to help improve the design and quality control of the final product.