Organic agriculture is a system of crop production without mineral fertilizers and synthetic pesticides. Natural fertilizers as manure, compost also green manure are widely used. For plant protection the natural insect predators and plants extracts are used. A lot of research made in Europe and Poland confirmed that crops from organic agriculture contained more bioactive compounds as flavonoids, carotenoids also vitamin C. The sweet red pepper is a good source of vitamin C, flawnoids especially rutin also carotenoids: capsorubin, capsantin, beta-carotene and lutein. Processing of fruits and vegetables is a good method to enhance diversity of diet. However, processing also decreases a level of bioactive compounds in comparison to the raw material. Therefore it was important to conduct the presented experiment. In the experiment two cultivars of sweet red pepper (Roberta and Berceo) from organiv and conventional cultivation were used. Fruits of all cultivars were picked up in this same maturity time and processed. After the pickling process fruits were divided into three groups: fresh (after pickling), pasteurized and pasteurized and stored 6 month. Fruit samples of each group were freeze-dried and chemically analyzed. The content of dry matter, witamin C, flavonoles, fenolic acids and carotenoids were carried out. The results obtained showed that pickled red pepper from organic production contained more vitamin C, flavonoles, fenolic acids, carotenoids and dry matter than the products from conventional production. After pickling process the organic samples were still richer in vitamin C, flavonoles, fenolic acids, lutein and dry matter than conventional ones. After storage period the content of bioactive compounds in the products has decreased; a decline was stronger in the organic samples than in the conventional ones.