Stored vegetable oil undergoes numerous processes, i.e., oxidation, hydrolysis, and thermal polymerization. As a result, its quality and organoleptic parameters deteriorate. The content of natural chlorophyll and carotenoid pigments determines the color of rapeseed oil. Almost imperceptible changes in the color of the oil may indicate the deterioration of its quality. Therefore, vegetable oils must be stored in the appropriate conditions to protect them against unfavorable factors leading to deterioration. This publication examines and describes the influence of storage temperature, type of packaging (clear glass, colored glass, PET), and presence of an oxygen-free atmosphere on the quality of stored cold-pressed rapeseed oil for three and six months. Changes in the following parameters were verified: the content of chlorophyll and carotenoid pigments, oil color (measured by the CIE Lab method), acid value, and radical scavenging activity (%RSA) by the ABTS (diammonium 2,2′-azinobis[3-ethyl-2,3-dihydrobenzothiazole-6-sulphonate) method. The decrease in the content of natural dyes was 7 to 87% after three months, depending on storage conditions, and after six months, from 12 to 97%. To determine which factors were responsible for the change in the physicochemical properties of the oil during storage, a principal component analysis (PCA) was performed.