AbstractBACKGROUND: The aim of this work was to study the effects of organic (O), low‐input (LI) and soilless (SL) cultivation on pepper nutritional quality and antioxidant activity. For that, 24 commercial greenhouses were selected following strict criteria in order to reduce the influence of environmental conditions and realistically reflect commercial production systems. Fruits were harvested at two maturity stages (green and red) and three harvesting times during two consecutive years.RESULTS: Pepper antioxidant activity mainly stemmed from water‐soluble compounds, including organic acids and phenolic compounds. Only some differences in sugars and malic and citric acid concentrations were detected between the O and LI systems. Sugars, phenolic compounds, ascorbic acid and hydrophilic antioxidant activity were higher in the SL system. In spite of these differences, overall differences between harvesting times or between years were far greater than those due to the cropping system.CONCLUSION: The main differences in the nutritional quality of pepper fruits were observed between the soil (O and LI) and SL (the most favourable) systems. The results highlight the importance of comparing different harvesting times and years in order to study the effect of cropping system on a specific crop. Copyright © 2009 Society of Chemical Industry