Vegetable nutritional quality is related to concentrations of antioxidants and other phytonutrients. In Iran, vegetables can be produced in soil in climate-controlled greenhouses. Limited information is available on the quality of greenhouse-grown vegetables compared to field-grown vegetables. Concentrations of Ca, Mg, P, K, Fe, Zn, Cu, Mn, and ascorbic acid in greenhouse- and field-grown bell pepper (Capsicum annuum L.), cucumber (Cucumis sativa L.), and tomato (Solanum lycopersicum L.) were determined. Mean fruit K, P, and Mg concentrations in greenhouse-grown bell pepper, cucumber, and tomato were greater than expected levels. Mean fruit K concentrations in greenhouse-grown bell pepper, cucumber, and tomato were lower than that in field-grown vegetables. Greenhouse-grown vegetables accumulated greater amounts of P in fruit compared to field-grown vegetables. More than 48%, 38%, 30%, and 54% of greenhouse vegetables were Fe, Zn, Cu, and Mn deficient, respectively. Field-grown vegetables had lower contents of Cu, Mn, Fe, Zn, and ascorbic acid compared to greenhouse-grown vegetables. Calcium, Fe, Cu, Mn, and Zn intakes through consumption of greenhouse-grown vegetables for population study groups accounted for a negligible fraction of the recommended daily allowance (RDA), whereas daily intake of ascorbic acid was greater than the RDA requirement. Intake of micronutrients and ascorbic acid from field-grown vegetables was less than that from greenhouse-grown vegetables. In general, the nutritional quality (contents of micronutrients and ascorbic acid) of greenhouse-grown vegetables was better than that of field-grown vegetables, although fruit micronutrient concentrations of field- and greenhouse-grown vegetables were lower than expected levels. The results indicated that bell pepper is an excellent source of ascorbic acid and potassium for humans. Despite a protected system of cultivation, poor fertilizer management in greenhouses could adversely affect the nutritional value of vegetables. Improved nutritional management in greenhouses could enhance micronutrient concentrations in these vegetables.