Footage from their meeting on Tuesday showed the first female head of the EU executive, the only woman in the talks, gesturing in disbelief and uttering a surprised sigh as Erdogan and European Council President Charles Michel took the two center-stage seats prepared, relegating her to an adjacent sofa.
"The president of the Commission was clearly surprised," said the EU executive arm's spokesman, Eric Mamer.
The Turkish government did not immediately respond to a request for comment.
In the past, three chairs were provided when the Turkish leader visited Brussels for talks with the heads of the Commission and the European Council, which collectively represents the bloc's 27 member states.
Mamer said von der Leyen decided to emphasize substance over form and in the conversation brought up women's rights and the Istanbul Convention on violence against women, from which Turkey withdrew last month.
Ties between Brussels and Ankara have been strained since a coup attempt in 2016 prompted a crackdown on civil rights in Turkey, but they are now testing a cautious rapprochement.