Soybean is the main source of crude protein (CP) and amino acids (AA) for poultry diets. However, the impact of bean damage on the nutrient and antinutrient content has not been well explored. This study aimed to determine the effects of raw soybean quality within four kernel damage categories (as is, good, purple damage, and completely damaged) and two protein levels (41.5 and 45.6% DM) on three α-galactosides, sucrose, non-starch polysaccharides (NSP), CP, AA, and trypsin inhibitor (TI) content. Soybeans from two CP levels were planted and harvested under similar conditions and classified into four quality categories based on kernel damage. NSP content, including solubility fractions, was determined by GC analysis of constituent sugars, while sugars and oligosaccharides were determined by ion chromatography. Other compounds CP, AA, and trypsin inhibitor content, were determined by NIRS. Data were analyzed using a two-way ANOVA in a completely randomized design. Interaction effects (P < 0.05) between protein level and bean quality were observed in all parameters evaluated, except for verbascose and methionine content. Regardless of the protein level, completely damaged kernels presented the lowest (P < 0.05) values for raffinose, stachyose, total α-galactosides, and sucrose compared to the good quality beans. In contrast, completely damaged soybeans presented the highest values (P < 0.05) for soluble, insoluble, and total NSP at both protein levels compared to soybeans from other quality categories. CP and AA were reduced as grain damage increased (P < 0.05). Still, 41.5% of CP kernels resulted in lower nutrient content than their counterpart at 45.6%. Additionally, the lowest TI was detected in kernels from the as-is group at 41.5%, while good and purple beans indicated the highest values. Intermediate responses were observed in beans from all categories at 45.6% CP. Kernels with 41.5% of CP resulted in 0.6 g more (P < 0.05) soluble NSP compared to 45.6% CP grains. The damaged group consistently demonstrated the lowest (P < 0.05) α-galactosides, sucrose, CP, AA, trypsin inhibitor, and soluble NSP, but showed the greatest content of total NSP.