Agriculture is an important source of anthropogenic emissions of the greenhouse gases (GHG), methane (CH4) and nitrous oxide (N2O), and crops can affect the microbial processes controlling these emissions in many ways. Here, we summarize the current knowledge of plant–microbe interactions in relation to the CH4 and N2O budgets and show how this is promoting new generations of crop cultivars that have the potential to mitigate GHG emissions for future agricultural use. The possibility of breeding low GHG-emitting cultivars is a paradigm shift towards sustainable agriculture that balances climate change and food and bioenergy security.