The demand for organic vegetables is increasing worldwide, which has led to the growth of organic agriculture. However, information on chemical composition and antioxidant activity in vegetables grown organically under controlled conditions remains uncertain. For this study, 3 vegetables widely consumed in Brazil were cultivated in controlled organic and conventional cultivation systems: lettuce, coriander and tomato. Their chemical composition, mineral concentration, phenolic compound content, flavonoids and antioxidant activity (AA) were evaluated. The analyses of chemical and mineral composition revealed differences between the cultivation systems. Organic lettuce presented higher content of ashes, calcium and potassium. A higher content of phenolic compounds and flavonoids was observed in most organic vegetables. Using the 2,2′-diphenyl-1-picrylhydrazyl (DPPH) assay, the organic tomato exhibited higher AA compared to conventional, while the ferric-reducing antioxidant power (FRAP) method showed higher AA for organic coriander and tomato than theirs conventional version. The correlation between bioactive compounds and AA was positive, higher and stronger for organic vegetables, considering phenolic compounds (including flavonoids) and DPPH or FRAP antioxidant activity. Principal Component Analysis (PCA) disclosed that organic lettuce and coriander were grouped according bioactive components. In general, organic vegetables showed better results for bioactive compounds and antioxidant activity.