The agricultural uses of nanoparticles continue to be considered as innovative methods that require more in-depth research into their impact on product quality. In our study, we investigated the effects of fertilizers containing metal nanoparticles (silver AgNPs and copper CuNPs) during the plant growth stage of winter rape cultivation, and in most experimental variants, with the exception of the (x2) application of AgNPs, we observed a decrease in the mass of one thousand seeds (MTS). The obtained result was 11.55% higher relative to the control sample in 2019, and also increased after the (x1) 4.36% and (x2) 11.11% application of CuNPS in 2020. The analyzed oxidative stability of the oil increased in both experimental years (2019–2020), with the highest values recorded after the (x1) and (x2) application of CuNPS—4.94% and 8.31%, respectively, in the first year of cultivation, and after the (x2) application of CuNPS—12.07% in the subsequent year. It was also observed that the content of polyphenols, flavonoids, squalene, tocopherols α and δ, chlorophylls, and carotenoids increased in the oil. Moreover, spectral FTIR analysis was performed on the oil samples obtained from cultivations sprayed with solutions containing Ag or Cu nanoparticles and revealed changes in several spectral regions with the maxima at ~1740, 1370, 1230, and ~1090 cm−1. Additionally, a FTIR analysis conducted in combination with multivariate analysis allowed us to classify the studied oils into the most similar groups and to study the structure of data variability. The conducted analyses revealed that the use of nanoparticles resulted in decreased size of the produced seeds and improved antioxidative properties of rapeseed oil.