One percent of the global population requires a gluten-free diet. With concurrent global warming and population growth, it is increasingly necessary to optimize the use of ingredients from resilient crops, such as tapioca. Tapioca flour is used in low proportions in bread due to its lack of gluten. Sourdough fermentation can enhance the nutritional value of bread but also causes a sour taste. Propionibacterium freudenreichii subsp. globosum can reduce food acidity while synthesizing several nutrients, such as vitamin B12. Aquafaba is a known hydrocolloid and prebiotic. Therefore, the objective of this study was to test the sourdough fermentation of a composite bread based on tapioca and brown rice flour, cultured with Lactobacillus lactis and Propionibacterium freudenreichii subsp. globosum enriched in aquafaba. The bread quality was measured instrumentally (hardness, volume, moisture content) and with a semi-trained sensory panel (focus group). The co-fermentation of the Lactobacillus lactis and Propionibacterium freudenreichii subsp. Globosum produced palatable bread, improving the appearance, taste, and texture in comparison to the yeast-leavened recipe. This co-fermentation also enabled shorter production times, reducing it from 1 h to 30 min. The addition of the aquafaba further improved the bread appearance, texture, and volume, although a bitter tasting crust was reported. The co-fermentation of the tapioca–brown rice composite flour with Lactobacillus lactis and Propionibacterium freudenreichii subsp. globosum produced acceptable bread, which could provide a climate-resilient solution to food sustainability. The aquafaba addition further enhanced such improvements and the baking performance, offering sustainability in terms of nutrition, sensory quality, and price.