Given the nutritional importance of peanuts, this study examined the free amino acid (FAA) and crude protein (CP) content in raw peanut seeds. Near-infrared spectroscopy (NIRS) was employed in combination with variable selection algorithms after successful reference data analysis using colorimetric and Kjeldahl methods. Ensuing the application of partial least squares (PLS) as a full spectral model, the genetic algorithm (GA), bootstrapping soft shrinkage (BOSS), uninformative variable elimination (UVE), and random frog (RF) models were tested and assessed. A comparison of correlation coefficients of prediction (Rp), root mean square error of prediction (RMSEP), and residual predictive deviation (RPD) was performed to appraise the performance of the built models. Using RF-PLS, an unsurpassed outcome was achieved for FAA (Rp = 0.937, RPD = 3.38) and CP (Rp = 0.9261, RPD = 3.66). These findings demonstrated that NIR in combination with RF-PLS could be utilized for quantitative, rapid, and nondestructive prediction of FAA and CP in raw peanut seed samples.