The European Commission announced the departure of Frans Timmermans, the first vice president and climate chief, hours after he was confirmed as the leader of a left-wing coalition for an upcoming Dutch election.
Mr Timmermans, 62, hopes to become the next prime minister of the Netherlands after spending close to a decade in Brussels, where he became a powerful figure in charge of the bloc's ambitious climate policies.
He previously served as Dutch foreign affairs minister between 2012 and 2014, during which he oversaw the aftermath of the shooting down by Russian separatists of Malaysian Airlines flight MH17 which killed 198 Dutch nationals.
“I want to become prime minister because I think together we can do politics differently than it had been done in the past few years,” Mr Timmermans said last month.
Mr Timmermans' term as EU executive vice president had been scheduled to end after next year's European elections but Ursula von der Leyen accepted his resignation.
The collapse of outgoing Prime Minister Mark Rutte's coalition over asylum issues triggered snap elections that will be held on November 22.
The politician is seen as a heavyweight contender from the left for the position of Dutch prime minister.
He was appointed to the top spot in the PvdA (Labour) and GroenLinks (GreenLeft) coalition after a ballot in which some 91 per cent of more than 37,000 party members backed his candidacy on Tuesday.
“An overwhelming majority has agreed to have Timmermans as leader,” the PvdA-GroenLinks coalition said.
There was no other candidate.
Ms von der Leyen thanked Mr Timmermans for his work, saying that his “excellent contribution and strong personal engagement” had enabled Europe to make “great strides” in its efforts to become “the first climate-neutral continent, and towards raising the levels of climate ambition globally”.
Mr Timmermans' announcement last month that he was a candidate to lead the leftist coalition raised questions about the EU's ability to influence negotiations at Cop28.
Ms von der Leyen said that vice president Maros Sefcovic would replace Mr Timmermans as executive vice-president for the European Green Deal.
She also temporarily assigned Mr Sefcovic, 57, the climate portfolio until the appointment of a Dutch commissioner. It was not clear whether the new Dutch official would assume the same post.
Mr Sefcovic, a Slovakian national, was appointed to the EU executive in 2009 as education and culture commissioner. He currently oversees EU relations with Britain and the EU's joint gas-buying programme to replace Russian gas supplies, after previously being in charge of the bloc's energy policy.
Ms von der Leyen said that: “our priority will be to strengthen industrial clean innovation, upgrading our grids and infrastructure for the energy transition and access to critical raw materials."
“The implementation of the European Green Deal requires an even more intensive dialogue with industry, stakeholders like forest owners, farmers, as well as citizens. And finally, we will continue to develop a stronger international strategy for the European Green Deal, in line with our economic and geopolitical interests,” added Ms von der Leyen.