Ecological niche models are being increasingly used to analyze the potential distributions of species, the effect of climate change, biological invasions, and other biogeography questions. A myriad of methods and workflows exist for ENM; some common steps are common to most of them, but there must be flexibility depending on the research question. Moreover, reporting the methodology and decision-making should give robustness to the conclusions. With the recent emphasis on reproducibility, a new set of practices, such as metadata recording, script-based applications, version control, and software version awareness can be included to the general workflows to ensure transparency. Here, we present modleR, an R package that implements such a reproducibility workflow for Ecological Niche Modeling. We also propose some guidelines for writing reproducible R code in ecology workflows in general.