El Niño is a major driver of fluctuations in tropical precipitation and fruiting production, with cascading effects on frugivores. As places get wetter, mutualistic networks tend to become more modular and less nested. In order to test the impact of severe floods and droughts caused by the El Niño cycle of 2015-2016 on nestedness and modularity of mutualistic networks, we determined the links between frugivorous bats and the plants in their diets by DNA barcoding bat faeces and used null models for our network comparisons. Despite the contrasting effects of droughts and floods in the dry forest and rainforest, respectively, we observed similar changes in network structure for both forests. We found higher values of modularity, but lower of nestedness for most networks comparisons. Over all we found higher nestedness in the dry forest than the rainforest and minimal difference between wet and dry season in the dry forest. A lower nestedness might reduce the number of species supported by the habitat as well as increase species competition. Although the increase in modularity might reduce the number of coexisting species in the environment, higher network compartmentalization leads to greater stability, slower spread of disturbance and smaller chances of having trophic cascades. Therefore, changes in network structure promoted by El Niño are likely to have dual effects on networks with some effects leading to greater stability while others to increasing competition.