Soybean seeds were germinated on an industrial scale after soaking for 0–56 h to produce a special additive for food industrial use. The germination process of three soybean varieties was monitored with near-infrared (NIR) spectroscopy based on changes in the amount, status, or character of the water. This paper evaluates the “waterless” NIR spectra of sound, germinated, and heat treated seeds to try to follow the fine details of the germination process. The germination process was analysed with the help of cluster analysis (CA), principal component analysis (PCA), and polar qualification system (PQS) as statistical and chemometric methods. PCA proved to be the most sensitive spectrum evaluation method to follow the fine details of germination. The applied NIR method is suitable for non-destructively, real-time monitoring of the non-linear nature of germination.