Display omitted •L. plantarum and F. sanfranciscensis produced sourdough with antifungal activity.•The antifungal activity varied depending on the substrate used and fermentation time.•The pH and organic acids fluctuated according to the substrate and fermentation time.•Sourdough from F. sanfranciscensis extended the shelf life of bread for 10 days.•Type III sourdough proved to be a promising biopreservative in bakery products. The potential biopreservative role of a Type III sourdough (tIII-SD), produced by starter cultures of Fructilactobacillus sanfranciscensis and Lactiplantibacillus plantarum ATCC 8014, was assessed for its antifungal activity in baking applications. Fermentation was carried out using different substrates to enhance the production of antifungal metabolites for 24 and 48 h. The tIII-SD samples were analyzed in relation to pH, total titratable acidity (TTA) and the production of organic acids. The water/salt-soluble extract of the tIII-SD was evaluated in relation to the inhibition potential against key fungi that contaminate bakery products including Penicillium roqueforti, Penicillium chrysogenum and Aspergillus niger. Finally, breads with 10 % of the tIII-SD were prepared and the fungi contamination was evaluated throughout the shelf life period. The lowest pH value in sourdough was obtained from 48-hour fermentation by L. plantarum. The saline extracts exhibited varying degrees of inhibition in the in vitro test; however, the greatest enhancement of this effect was obtained when whole wheat grain flour was used. The tIII-SD crafted from a blend of wheat and flaxseed flours and fermented with F. sanfranciscensis for 48 h (BSWF48h-FS), demonstrated superior performance compared to other formulations. This variant exhibited a total shelf life of 10 days, suggesting that the utilization of tIII-SD could serve as a viable alternative for natural antifungal agents, proving beneficial for the bakery industry.