We analysed physical and chemical properties of seeds and oils from different cultivars of winter rapeseeds (‘Markus’, ‘Bios’ and ‘Feliks’) that were cultivated using bio-gas natural manure (digestate) or with a commercially accessible Yara NPK 5014-28 (NPK) fertilizer, both of which were analyzed for element content. Seeds produced without use of fertilizers were taken as control. Prior to cold-pressing of oils, seeds were analyzed for fatty acid content. Cultivar ‘Bios’ breed with use of digestate showed a lower amount of oleic acid (C18:1), while the ‘Feliks’ cultivar had higher content of this fatty acid and lower amounts of linoleic acid (C18:2) as compared to respective controls. In the case of the application of NPK fertilizer, the increase in C18:1 was observed for the cultivars ‘Markus’ and ‘Feliks’. In the latter the decrease in the content of C18:2 was observed as compared to control. The oils were analyzed monthly for photosynthetic pigment content and oxidative stability as well as color during a storage period of three months. Oils contained similar amounts of chlorophylls and carotenoids. Oils derived from seeds produced with the use of commercial NPK fertilizer were characterized with higher oxidation stability (induction time) as compared to digestate. Gradual darkening of the oils was observed. Statistical analysis (p<0.05) showed significant correlation between all the color parameters and term of measurements as well as with the applied fertilizer.