One of the potential major impacts of Bioenergy production - and one of the most serious threats to biodiversity - is the conversion of grasslands and tropical forests and other biodiversity rich zones into monoculture croplands.

The Convention on Biodiversity target to halt the loss of global biodiversity requires the protection of land with high conservation values and ecosystem services. The cultivation of feedstocks should be excluded from such areas unless it can be proven they protect or enhance biodiversity. Further work is required to identify such areas beyond those that are already protected by law through the CBD, the Ramsar Convention or other international or regional agreements. Tools to do so include biodiversity mapping, both from the top down via GIS data and bottom up, involving local populations.

Two particular issues with bioenergy and biodiversity are the use of genetically modified organisms (GMOs), and the introduction of feedstock plants that may be considered invasive species. For both issues, careful assessment of possible consequences and their risks is essential.