Consumers are more and more interested in organic foods for they believe they are both safer and qualitatively more valuable. In many studies, it was proved that vegetables and fruits from organic production usually showed more favourable parameters of their pro-health and nutritional quality than conventional crops, however, so far, there are no studies on the quality of fruit and vegetable preserves made of organic products. Therefore, in this paper, some selected parameters characterizing the nutritional quality of organic and conventional apple preserves (juices and mousse) were compared. The investigated preserves (juice and mousse) of organic apples contained a significantly higher level of polyphenols and showed a higher antioxidant capacity than the preserves made of conventional apples. This result suggests a potentially more favourable biological value of organic fruit preserves. Pasteurizing and storing the preserves caused that the content of polyphenols and the anti-oxidant capacity of apple juice and mousse significantly decreased. The highest content of polyphenols and the highest anti-oxidant capacity was found in preserves made of the Jonagold apple cultivars, whereas the medium – in the Cortland apple cultivars, and the lowest – in the Idared cultivars.