After Ursula von der Leyen met Rishi Sunak to discuss a Northern Ireland Brexit deal, she will have tea with King Charles at Windsor Castle.
According to Buckingham Palace, the meeting was planned on the advice of the administration.
It was "fundamentally" a decision for the King, according to Number 10.
However, there have been cautions to avoid involving the monarch in a contentious political debate.
Former cabinet minister and Brexit supporter Jacob Rees-Mogg, a member of the Conservative Party, said it was "constitutionally unwise to involve the King in a matter of immediate political controversy.".
The meeting would run the risk of "dragging the King into a hugely contentious political issue," according to Sammy Wilson, chief whip of the Democratic Unionist Party.
However, the King's recent meetings with foreign dignitaries like the presidents of Poland and Ukraine who were in town, Andrzej Duda and Volodymyr Zelensky, were compared by the prime minister's official spokesman to his encounter with Ms. von der Leyen.
The spokesperson for Number 10 said, "The King should decide those things.".
The government advises that the King meet any visiting world leaders, and the King is happy to do so, according to a palace spokesman.
A new Brexit agreement for Northern Ireland had been reached, a senior government source told the BBC at around 14:20 GMT, ahead of the meeting.
By claiming that the meeting in Windsor between the King and the president of the European Commission was "separate" and "not part" of the discussions over the Northern Ireland protocol, the EU attempted to set the meeting apart from political negotiations.
According to sources at Buckingham Palace, the King and the visiting world leader were meeting as usual, and this meeting would build on their prior encounters with Ms. von der Leyen.
A larger agenda, including discussions about climate change and Ukraine, was mentioned for the meeting at Windsor Castle, where tea will be served and pictures will be taken.