Soybean [Glycine max (L.) Merr.] is an important animal and human food source, mainly because of its high protein and oil concentrations. However, there is a need to improve the quality of soybean protein and oil. The objectives of this study were to (i) determine the potential use of near infrared reflectance spectroscopy (NIRS) for amino and fatty acid analysis in soybean seed and (ii) compare NIRS amino and fatty acid equations developed with ground‐seed and whole‐seed soybean samples. A total of 90 NIRS calibration samples and 26 NIRS validation samples were used for NIRS equation development and validation, respectively. All 116 soybean samples were grown at St. Paul and Rosemount, MN, in 1994 and 1995. Seventeen amino acid and five fatty acid NIRS equations for both groundseed and whole‐seed soybean samples were developed using the calibration samples. Validation of these NIRS equations showed a wide range for bias (−1.7 to 3.2 g kg−1), standard error of prediction corrected for bias [SEP(C)] (1.4 to 13.1 g kg−1), and coefficient of determination (R2) (0.38 to 0.85) for all ground‐seed NIRS equations, and a broad range for bias (−3.1 to 4.2), SEP(C) (2.6 to 17.8), and R2 (0.06 to 0.83) for all whole‐seed NIRS equations. It was concluded that NIRS could be used as a gross screening method for many amino and fatty acids contained in soybean seed. Additionally, NIRS was more accurate for amino and fatty acid analysis of ground‐seed than wholeseed soybean samples.