Then the Parliament will have to agree as well, and we can see which parties there voted in favour, which you can take into account in the next European elections.
The Commission is toughest to hold accountable. The Commissioner pushing it (Ylva Johansson in this case) was nominated by a country's (Sweden, in this case) government, so Swedish voters could hold the parties in that government accountable in their next national election, I suppose, but that's a very weak signal.