This study aimed to assess the effects of cultivation system (organic and conventional) and modified atmosphere packaging (MAP) treatments on quality characteristics and bioactive compounds of tomato fruit (Solanum lycopersicum cv. Sencan 9) stored in cold storage conditions, at 8 degrees C +/- 0.5 degrees C and 90% +/- 5% relative humidity, for 21 days. At the end of the cold storage period, lower weight loss and respiration rates were measured in the organically produced fruit compared with the fruit produced in the conventional production system. On day 14 and 21 of storage, higher firmness was measured in the conventional- and organic-MAP treatments and in the conventional-unwrap treatment than in the organic-unwrap treatment. On day 7, L* and hue angle measured in organic-MAP were significantly higher than in the other treatments. At the end of the cold storage period, higher soluble solids content, vitamin C, total phenolics, total flavonoids, and antioxidant activity were recorded for the organic tomatoes, compared with the conventionally grown fruit. The highest and lowest concentrations of total flavonoids and antioxidant activity were determined in organic-MAP and conventional-unwrap treatments, respectively. In conclusion, it was shown that the quality of the tomatoes grown in the organic production system and stored in MAP maintained higher quality characteristics during the cold storage period.