Growing demand for gluten-free (GF) products promotes developing biotechnological strategies to enhance bread quality. Sourdough fermentation with lactic acid bacteria (LAB) offers potential to improve safety, functionality, and sensory properties of GF baked goods. This study evaluated Fructilactobacillus sanfranciscensis isolated from traditional sourdough for fermenting GF flours (rice and maize) and application in bread production. pH, total titratable acidity, LAB counts, and enzymatic activities were assessed. Sourdough with the highest phytase activity was selected for GF bread formulation. Fermentation caused more pronounced acidification in rice sourdough than maize. The highest L(+)- and D(–)-lactic acid levels were detected in maize sourdough. Rice sourdough showed highest amylase (0.43 U/g), phytase (46.57 U/g), and xylanase (41.52 U/g) activities; maize sourdough had the highest protease activity (0.093 U/g) and LAB count (8.68 log10 CFU/g). Different amounts of LAB-fermented sourdough were used in bread production. Increasing sourdough reduced dough and crumb pH and increased TTA without significantly affecting crumb porosity. Sensory evaluation showed sourdough improved sensory characteristics and acceptability of GF bread, depending on the sourdough amount. These results demonstrate LAB-fermented sourdough’s potential to improve gluten-free bread quality.