Oilseed rape (Brassica napus L.) is one of the most important oilseed crops in temperate climates. Erysiphe cruciferarum is an important disease of oilseed rape and causes crop loss in warmer areas of Europe. The research investigated the effect of nitrogen fertilizer and fungicidal treatment against powdery mildew infection caused by E. cruciferarum of oilseed rape on seed components, including protein, oil, oleic acid, linolenic acid and undesirable substances such as sinapic acid esters (SAE) and glucosinolates (GSL), using near infrared spectroscopy (NIRS). Five susceptible oilseed rape varieties were employed in this research using four treatment groups: no nitrogen fertilization and no fungicidal treatment (N-0 - F-0); no nitrogen fertilization but fungicidal treatment (N-0 - F-1); and nitrogen fertilization but no fungicidal treatment (N-1 - F-0); nitrogen fertilization and fungicidal treatment (N-1 - F-1). Nitrogen fertilization increased the protein, but lowered the oil content, of the seeds. Fungicidal treatments significantly increased oil contents in all varieties tested, however reduced protein levels in fertilized and non-fertilized plots. The level of linolenic acid did not change significantly in any plots of any treatment combinations; a similar result was observed in the level of oleic acid in most of the genotypes. Nitrogen fertilization increased GSL and SAE levels, whereas fungicidal treatment had no effect. Our findings demonstrated that nitrogen fertilization can markedly influence some quality parameters in oilseed rape; however, the application of fungicides reduced side effects of nitrogen fertilizer and resulted a reduction on GSL, SAE and protein contents but an increase on total oil and oleic acid contents.