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Introduction: Millets, owing to their rich nutritional and low-to-moderate glycemic index values, are termed superfoods; however, some anti-nutritional factors, such as tannins, limit the absorption of micro and macronutrients. Non-thermal processing technologies, such as fermentation, can improve nutrient content and reduce these anti-nutritional factors. Methods: The effect of a controlled submerged fermentation of whole grain sorghum, pearl millet, and dehusked Kodo millet using mixed lactic acid bacteria (LAB) culture in tofu whey-based media on the proximate, antioxidant, tannin content, vitamin B, amino acids profile and estimated glycemic index (eGI) of different millets were evaluated. Results: The protein content (2–12.5%), carbohydrate content (2–13.6%), antioxidant activity (3–49%), vitamin B complex, amino acid profile (89–90%), and eGI of whole grain sorghum, pearl millet, and dehusked Kodo millet improved due to LAB-assisted submerged fermentation. In contrast, fat (4–15%), ash (56–67%), crude fiber (5–34%), minerals, tannin and resistant starch content decreased due to LAB fermentation. Conclusion: Controlled LAB fermentation can improve the nutritional quality of sorghum and millets while reducing anti-nutritional factors. This non-thermal process can be adopted industrially to produce more palatable and nutritionally superior millet products.