The EC said the proposed scheme would support its mission to reach the 2020 renewable energy targets.
"Greece will bring down costs for renewable energy with competitive auctions to support renewable electricity generation," said commissioner Margrethe Vestager, who is in charge of competition policy in Europe.
According to the EC, in 2018 Greece will organise separate auctions for wind and solar projects to judge the market potential.
Then from 2019, joint auctions will be held to increase competition.
Support of other renewable technologies "will be subject to auctions as soon as they become more mature in the Greek electricity market", the EC said.
Greece had approximately 2.3GW of wind capacity installed at the end of 2017.