The common bean is an important staple food in Colombia with diverse nutritional content and environmental benefits. The most important climatic risk confronted by common bean production in Colombia is El Niño Southern Oscillation (ENSO) since its two extreme phases —El Niño and La Niña— increase the intensity and variety of abiotic and biotic stresses in the region. Using information from the Food and Agricultural Organization (FAO) for the period 1991–2018, we test whether pre-2030 ENSO has had a negative impact on common bean production in Colombia using a Prais–Winsten regression model. We find that common beans’ yields have been negatively affected by El Niño, but not by La Niña. Moreover, short-run ENSO-induced deviations in the growth rate of precipitation with respect to its long-run value reduce yields and increase farmers’ income from common bean production. These results have two important implications. From a modelling standpoint, we find that precipitation has a non-linear relationship with yields and incomes, implying that second-order effects should be incorporated in any analysis of the effects of climatic variables on agricultural production. From a policy perspective, our results suggest a need for countercyclical polices to counteract price spikes of common beans in the Colombian market since, when they occur, they tend to over-compensate the reduction in yields, which reduce common bean consumers’ purchasing power and food security.