Exposure of lactic acid bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress; consequently, microbes develop adaptive responses. In this study, we investigated the physiological and proteomic responses of LAB and yeast to acid stress and their application in food fermentation. The physiological and proteomic responses of Lactobacillus amylovorus LS07 and Candida kefyr YS12 to acid stress were measured using turbidimetry, SDS-PAGE, and LC-MS/MS. The technique previously reported by the Association of Official Analytical Chemists (AOAC) was employed to evaluate the physicochemical and organoleptic properties of sorghum gruel fermented using LAB and yeast alone and in combination as starter cultures and spontaneous fermentation as a control. The growth of L. amylovorus LS07 was optimal at pH 1.0, and that of C. kefyr YSI2 was optimal at pH 4. An increased intensity of 30S ribosomal protein S2 (L. amylovorus LS07) and 6-phosphogluconate dehydrogenase (C. kefyr YS12) was observed at pH 1 and 4, respectively, suggesting increased microbial metabolism, thereby reducing the stress. Sorghum gruel produced with combined starters had the highest crude protein (10.94%), iron content (0.0085%), and organoleptic acceptability (7.29), which was significantly different from the products produced with the single starters and the control. The combined starter (L. amylovorus LS07 and C. kefyr YSI2) adapted to stress yielded foods with improved sensory properties, minerals, and reduced anti-nutrient contents.