The study determined the internal quality (the total phenol, sugar, organic acid contents, antioxidant activity, and mineral components) and physical parameters in the flesh of red beetroots produced in different production systems (conventional, integrated, organic, and control) using established methods. Organic cropping of red beetroot plants significantly reduced the yield by 27% of some macro minerals (P at 23.1, K at 13.1, and Mg at 7.7%) in comparison with conventional cropping but increased the ascorbic acid by 23.3%, antioxidant activity by 30.3%, and some micro minerals (Na at 39.1, Cu at 5.0, Fe at 17.9, Mn at 3.4, and Zn at 2.1%). The organic system can also result in better economic feasibility under assumption that price and expected yield are achieved. The results showed that a decrease in nitrogen supply, which is inherent in organic cropping, enhances the levels of secondary metabolites and micro minerals, which are associated with increased free radical scavengers and antioxidant activity in plant tissue.