Black Sigatoka, caused by the leaf fungus Mycosphaerella fijiensis Morelet, is a major constraint to banana production around the world. In Ecuador, the biggest banana-exporting country in the world, this disease has become increasingly aggressive. This has resulted in more fungicide applications, which have significantly increased costs in production and for the environment. Consequently, many banana growers have shifted to organic production, which produces greater economic returns as a result of higher sale prices. In addition, production costs are lower as no fungicides are applied. These organic bananas receive substantial amounts of organic products. This study describes the black Sigatoka disease and nutrient status in an organic banana plantation and compares it with a conventionally fertilized and fungicide-treated plantation. Black Sigatoka symptoms were evaluated in the vegetative and flowering stages under both production conditions and in vitro conditions. Univariate and multivariate descriptive statistics were used to analyze the parameters. Disease symptoms were more severe in leaves from the organic field than in leaves from the inorganic field, but the nutrient status (soil and foliar) did not differ between the two farms. Banana plants from the organic farm had 12 functional leaves at flowering and eight functional leaves at harvest. Average banana yields were over 40% lower for organic versus inorganic management; however, the average price received for organic bananas was over two times higher. Profit–cost analysis has shown that the organic banana farm was substantially more profitable than the inorganic one during the time period analyzed. These results indicated that bananas can be grown commercially without fungicides, and the lower productivity levels are compensated by higher prices of organic fruits in international markets. In addition, organic production has beneficial impacts on social and environmental issues.