I think a good US comparison would be the US Cabinet, which (AFAIK - I'm not from the US) are not themselves elected, but are appointed by the President and confirmed by the Senate.
The President and the members of the Senate are elected. (I think you probably already know this!)
Similarly with the EU. The President of the European Commission is proposed by the European Council, which is composed of the heads of state or government of all the member states (all subject to elections in their own countries, according to that country's laws), and elected by the European Parliament, all of whose members are elected. The European Parliament also has the power to dismiss the President and the entire EU Commission.
So it seems to me that Ursula von de Leyen, the current President of the EU Commission, is no more or less democratically accountable that (say) the current US Secretary of State - Antony Blinken or (if you're of a Republican persuasion) Mike Pomeo, a previous incumbent from the Trump era.