Paraná and São Paulo are two important common bean (Phaseolus vulgaris L.) producing Brazilian states. Fungal diseases are among the various biotic stresses that impair common bean yield. Fungus-resistant common bean cultivars showing good performance have been recommended for these states, but the application of fungicides is still necessary in many cases to assure grain yield and quality. Therefore, the rational management of agrochemicals is a research priority due to the potential risks to the environment and the costs associated with unnecessary applications. This study developed strategies for decision-making regarding the use of fungicides in disease management in common beans under the El Niño-Southern Oscillation (ENSO) phenomena. The field trials were classified based on ENSO phenomena (La Ninã, El Niño and Neutral). The genotype yield response was analyzed by a linear model considering two scenarios: with ENSO and without ENSO. Including the ENSO climate phenomena in the analysis helped to better discriminate the situations in which the use of fungicides in the common bean crop results in significant productivity gains. For example, the occurrence of El Niño tended to be associated with increased fungal disease pressure, whereas, on the contrary, in its absence, the disease pressure was lower, which should be considered when selecting resistant genotypes. The results of this study may help farmers and decision-makers to optimize fungicide application in the main common bean producing regions of Brazil, minimizing the impact of the common bean crop on the environment. Display omitted •ENSO in trial analysis help to discriminate when fungicides results in gain in yield.•Plant breeding programs should consider the climate data in the evaluation trials.•A strategy for fungicide application should consider the climate phenomena.•El Niño increases the environmental pressure for fungal diseases.