This study analyzed the effect of various treatment methods on the nutritional quality of soybean flour, as well as the study on the impact of soy flour and oats on the physico‐chemical and sensory properties of the prepared biscuit containing oats and soy flour. Six formulations of biscuit were designed using a design expert, prepared with soy flour, wheat flour, and oats flour. Autoclaved and germination followed by roasted soy flour were used differently with wheat and oats flour to prepare six samples of biscuit each. The soy flour was varied from 5% to 20% and oats flour from 5% to 15%, respectively. Raw soybean had tannin content of 500 mgTAE kg−1 and phytic acid content of 13,280 μg kg−1. Tannin content of autoclaved, germinated, and germination followed by roasted soybean was reduced by 22%, 38%, and 52%, respectively. The phytic acid content of soybean autoclaved, germinated, and germination followed by roasted was reduced by 30.6%, 46.8%, and 59.3% respectively. Sample D was found to be the best (p < 0.05) of the two superior samples (i.e., D and D′). The best product had 1.6% moisture, 23.2% crude protein, 25.2% crude fat, 1.3% total ash, 5.6% crude fiber, 44.8% carbohydrate, 120 μg kg−1 phytic acid, and 50 mgTAE kg−1 tannin content. The biscuit prepared from germination followed by roasted soybean flour had less anti‐nutritional factor compared with biscuit prepared from autoclaved soybean flour. Thus, in a composite flour, flour prepared after processing of soybean can be used to prepare nutritious and consumer appealing biscuit, with significant reduction in the quantity of anti‐nutritional factors.