Nitrate leaching frequently is attributed to the excessive application of mineral nitrogen fertilizers and also to the organic matter incorporated in the soil. A lysimeter experiment was conducted in a greenhouse to evaluate nitrate leaching and pepper productivity in an organically fertilized substrate (prepared by application of 4 kg · m−2 horse manure and subsequent solarization) to which three different doses of mineral fertilizers were added at 0 (T1), 157 (T2), and 313 (T3) kg N · ha−1. The results confirmed the high contribution of organic matter to nitrate leaching, although nitrate losses in T2 and T3 were around 33% and 100% greater than in T1. Furthermore the application of mineral fertilizers (T2 and T3) combined with organic manure led to a decrease in pepper fruit productivity. The use of porous ceramic water samplers for measuring fertilizer leaching is questioned. The results also point to the need for a revaluation of irrigation and N fertilization procedures when organic manure is used in order to improve pepper yield and reduce the contamination of ground water by nitrates.