Coffee agroecosystems under organic and conventional management systems were studied in three different altitudinal floors in La Convencion Province, Cusco, Peru. The Shannon index, equity index, index of dominance, incidence of pests, amount of soil microorganisms, chemical soil characteristics, yield, quality and profitability of coffee agroecosystems were evaluated. No statistical differences were found between organic and conventional agroecosystems for most of the variables evaluated, except for organoleptic quality. The results were similar for most variables studied when the effect of altitude was evaluated, except in the incidence of Hipothenemus hampei (Ferrari), Hemileia vastatrix (Berk. and Br.) and Mycena citricolor (Berkeley y Curtis), soil pH and CIC values. The yield of dry parchment coffee, export coffee and price and production costs were higher in organic production systems. The highest financial profitability corresponded to the organic production system at an altitude of 1600 masl.