Sourdough fermentation is rarely used for gluten-free flatbread (GFFB), a product that is challenging to produce, especially when using high-fiber ingredients that bring nutritional benefits but lead to physical deterioration. The aim of this study was therefore to evaluate the fermentation performance of carob flour (CSPF), proso millet flour (PMF), and proso millet bran (PMB) individually and in combination with Limosilactobacillus fermentum and Kluyveromyces marxianus (LF + KM) and to compare the performance of LF + KM with a commercial starter (LIVENDO® LV1). A mixture design (n = 13) was used to evaluate the fermentation performance of LF + KM (total titratable acidity (TTA); lactobacilli and yeast growth; acetic and lactic acid, fructose, glucose, and saccharose content) at 35 °C for 16 h. The comparison of LF + KM with LV1 fermentation was based on the acidity rate, fermentation quotient, TTA, and finally by determining the physical properties (texture, shape, color) of a rice–corn GFFB in which 10% of flour was supplemented with the sourdoughs. PMB promoted the growth of lactobacilli and the production of organic acids, especially in combination of CSPF and PMF. The optimum flour ratio was 2.4:1:1.2 (PMB:PMF:CSPF). LF + KM shortened the sourdough fermentation time by 2.5 times compared to LV1. The use of LF + KM sourdough reduced the hardness (32%) and chewiness (28%) of the GFFB, while the volume (35%) was increased compared to LV1 sourdough. This study shows the potential of using local alternative flours in sourdough fermentation for the production of GFFB.