How ecological interactions vary across spatial and environmental gradients has received increasing attention in recent years, contributing to the revelation of the drivers of biodiversity. However, it is still unclear how the structure of ecological interactions varies across large spatial scales and which climatic factors are associated with such variation. Here, specific predictions were derived and tested to evaluate how climatic factors and latitude are associated with the structure of bat-fruit interaction networks throughout the Neotropical region. For each study site (n = 44 sites, encompassing 48 degrees of latitude), four metrics were used to describe the network structure (i.e., network size, connectance, modularity, and nestedness). In general, an increase in modularity and a decrease in connectance and nestedness was observed towards lower latitudes and in sites with lower precipitation seasonality. Moreover, plant richness within networks increased towards lower latitudes and in sites with higher annual precipitation, whereas bat richness increased at lower latitudes and in sites with lower precipitation seasonality. These findings partially confirm both energy and seasonality hypotheses and suggest that fruit-bearing plant richness and fruit availability associated with annual precipitation and precipitation seasonality can be important correlates shaping the structure of ecological interactions throughout the Neotropical region.