Organic production is one of the fastest growing food sectors globally. However, average yield in organic vegetable production is up to 33% lower than in conventional production. This difference could be due to higher fertilization rates in conventional, compared to organic, farming. We aimed to compare yield and quality characteristics of carrots produced under equal nitrogen fertilization rates over four years in organic and conventional conditions. We found a 14.5% higher marketable, and 10.0% lower discarded, yield in the organic compared to the average conventional treatments. In addition, carrots managed organically had 14.1% lower nitrate and 10.0% higher vitamin C content than carrots managed conventionally. There were no convincing effects of cultivation system on the nitrogen, total sugar, or dry matter content of carrots. Organically managed carrots were free of pesticide residues, while several residues were found in carrots managed conventionally. Our study reveals that organic management of carrots may exceed that of conventional methods in yield and several quality characteristics, while being free of pesticide residues. Organic fertilizer gave an advantage over mineral fertilizer, when equal rates of nitrogen were used in both production systems.