Employing biotechnology processing in the manufacturing of baked goods with underutilised gluten-free cereals is deserving of marked interest to get new niche products. This study aims at determining the influence of sourdough made with starter cultures on the nutritional and sensory characteristics of cookies produced with acha flour. Sourdough containing lactic acid bacteria and yeast starters were added as ingredients for making acha-based cookies. Sourdough increased the spread ratio of the cookies. Fructilactobacillus fructivorans and Candida tropicalis as mixed starters gave the highest values (6.52 AE 0.06 and 2.21 AE 0.27, respectively) for crude protein and ash. Sourdough addition and the type of starter culture used for the fermentation influenced the mineral composition of cookies (P < 0.05). The most overall acceptable was SBTC, made with only C. tropicalis sourdough. Utilisation of acha with sourdough addition is recommended for making cookies with improved qualities and promoting the locally grown cereal for potential health benefits.