AbstractBACKGROUND: The influence of farming systems on fruit quality remains controversial and the different aspects associated with each agricultural management system need to be studied separately to elucidate any specific effect on fruit quality. To this end, a greenhouse experiment was conducted to examine the effect of the usual fertilisation guidelines for pepper cultivation on the nutritional quality of fruits (sugars, vitamin C, total phenolic compounds, chlorophylls, total carotenoids and antioxidant activities in the hydrophilic (HAA) and lipophilic (LAA) fractions). Treatments included manure amendment combined with synthetic fertiliser applied at the rates recommended for organic (T1), low‐input (T2) and conventional (T3) practices.RESULTS: Pepper composition was not affected by increasing mineral fertilisation. In addition, treatment had no significant effect on HAA or LAA. The antioxidant activity of both the hydrophilic and lipophilic fractions increased from the green to the red stage of ripening. HAA contributed about 80% of the total antioxidant activity.CONCLUSION: Pepper response to mineral fertilisation seems to be less pronounced than that of other fruits, since antioxidant concentrations did not increase with increasing fertiliser application. Antioxidant activity in pepper was mainly linked to hydrophilic compounds (vitamin C and phenolic compounds). Ripening was the most important factor determining the fruit antioxidant composition. Copyright © 2009 Society of Chemical Industry