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The aim of this study was to evaluate the effect of three organic fertilization sources on the agronomic and biochemical qualities of four genotypes of Serrano pepper. The experiment was performed at the field in Gomez Palacio, Durango (Mexico). The capsaicinoids (CAP’s) are compounds responsible of the pungency of the peppers, and they are valuable for health and food and cosmetic food. The organic treatments applied were: solarized bovine manure (60 Mg/ha), vermicompost (10 Mg/ha) and poultry manure (5 Mg/ha). A non-fertilized treatment was used as control. The evaluated variables were: length, diameter and individual weight on fruits, and capsaicin and dihidrocapsaicin concentrations in pulp and seeds. The results showed significant differences among treatments in the evaluated variables, as well as regarding the fertilization treatments. The genotype Don Diego I fertilized with vermicompost had the larger fruit weight, while the genotypes Don Vicente and Don Diego I showed the highest values of length, diameter and individual fruit weight without considering the fertilization source. Regarding the 3 organic treatments applied, the genotype Don Vicente fertilized with poultry manure had the highest concentration of capsaicinoids. The organic materials evaluated can be applied as a nutritional source for production of Serrano pepper in arid zones, obtaining the highest fruit quality by fertilization with vermicompost. The genotypes Don Diego I and Pepper Don Vicente obtained the highest capsaicinoid concentration.