In the present study, four tomato cultivars were grown under organic and conventional conditions in separate unheated greenhouses in three consecutive years. The objective was to assess the influence of the cultivation system on the content of individual polyphenols, total phenolics, and antioxidant capacity of tomatoes. The fruits were analyzed for total phenolic content by the Folin-Ciocalteau method and antioxidant capacity by the DPPH free radical scavenging assay. Individual phenolic compounds were analyzed using HPLC-DAD-MS/MS. Among 30 identified and quantified polyphenols, significantly higher contents of apigenin acetylhexoside, caffeic acid hexoside I, and phloretin dihexoside were found in all organic samples. The content of polyphenols was more dependent on year and cultivar than on cultivation conditions. Generally, the cultivation system had minor impact on polyphenols content, and only a few compounds were influenced by the mode of cultivation in all tested cultivars during all three years.