The commission has approved a number of certification procedures for biofuel companies to seek approval of their products, the BBC reported Tuesday.
Biofuel companies can seek certification from one of the EU procedures or from a similar national scheme, the commission said.
Biofuels are seen as an important part of the EU strategy to cut CO2 emissions, but the feedstock crops are controversial and have replaced forests in some countries, harming biodiversity.
They are also seen as sometimes displacing food crops.
The sometimes damaging impacts of biofuel production were "a real concern ... particularly in the big producing countries, south-east Asia and in South America," EU Energy Commissioner Guenther Oettinger said.
Under the new certifications, companies importing or producing biofuels will have to prove they meet the EU's strict criteria for sustainability and emit at least 35 percent less greenhouse gases than fossil fuels, the BBC reported.