Replicated field trials at three matched farm pairs in southern and central Taiwan were established in October 2004 and 2005 to compare fruit quality and nutritional parameters of tomatoes grown on-farm under organic versus conventional management systems in tropical and subtropical environments. Two processing tomato varieties were evaluated using a randomized complete block design at each of the farms. Aggregation of farms by type (organic vs conventional) across two years resulted in no significant differences between organic and conventional farming systems for all tomato fruit parameters measured, including quality (pH, soluble solids, acidity, and color), content of bioactive compounds with antioxidant activity (beta-carotene, lycopene, ascorbic acid, and total phenolics), and antioxidant activity. This study indicated no consistent effect of the farming system on tomato fruit parameters. Farm management skills combined with site-specific effects contributed to high lycopene levels, and the choice of variety significantly influenced the content of bioactive compounds, particularly ascorbic acid and total phenolics.