The increasing demand of organic agriculture (OA) is based on the consumer’s belief that organic agricultural products are healthier, tastier and more nutritious. The effect of OA and conventional agriculture (CA) methods on the elemental compositions of green and red sweet peppers were studied. The highest concentrations of Ca, Cu, K and P occur in peppers from OA in both states of ripeness, with emphasis on Ca and K contents. Furthermore, the principal component analysis (PCA), points out to a clear separation, regarding concentrations, between peppers from OA and CA. The average fruit weight is higher in OA, 141 g versus 112 g in CA. Regarding productivity, CA reaches a value of 30.1 t/ha, 7% higher than the value observed for OA, i.e., 28 t/ha. Peppers from CA, exhibited greater protein content than those which originated from OA, regardless of the ripening stage, but not more ashes. Regarding nutritional ratios, the ripening stage and the production mode, can be important for an adequate choice regarding a more balanced Ca/P ratio, and the studied variety contained high Ca values ranging between 1009 and 1930 mg.kg−1. The PCA analysis also revealed that Mn and Fe are inversely correlated, confirming the importance of the Mn/Fe ratio evaluation in nutritional studies.