Sweet pepper plants were grown in a greenhouse under three different cultivation methods (organic, integrated and conventional farming). During the crop cycle, plant growth and especially yield and fruit quality parameters were monitored to determine the effects of the different fertilization strategies. Plant fresh weight and total leaf fresh weight were progressively reduced, relative to the other treatments, in the organic treatment compared with the conventional, and at the end of the crop cycle these parameters were reduced by 32.6 and 35% respectively. This reduction in growth was directly correlated with plant nitrate concentration and, at the end of the study, nitrate concentration was reduced almost completely in the organic treatment. Despite the important effect on growth, no significant differences in total marketable yield were observed between conventional and organic farming, although integrated farming showed the highest yield in the extra and first class fruit categories. Organic farming increased antioxidant activity but reduced both chlorophylls and β-carotene. Fruit firmness, pericarp thickness, pH and total soluble solids content showed higher values with the organic method, but these differences were not significant with respect to the conventional method. Our results show the advantages of the organic fertilization, from both environmental and economic perspectives, if proper dosage is added to the crop and the demonstrated buffer capacity of these plants, with respect to maintaining yield under nutrient depletion at later stages of development, is taken into account.