In a letter sent this week to European Council president Donald Tusk, Macron started the official process of France recognising the EU's 12-star flag.
That would also mean recognising the European anthem - the Ode to Joy from Beethoven's Ninth Symphony - the EU motto "United in diversity", the euro as Europe's currency and 9 May as Europe Day.
"I'm very happy ... as some people today seek to create divisions and to turn France in on itself, to confirm France's attachment to the European flag and anthem," he declared in Brussels before the summit started.
Left-wingers want flag out of parliament
The move is the president's response to an attempt by the hard-left France Unbowed (LFI) party to stop the flag being flown at the French parliament.
Last week the party's MPs submitted an amendment stipulating that only the French tricolore and the UN's flag could be displayed there.
LFI leader Jean-Luc Mélenchon even argued that the EU flag is a religious symbol because its designer, Arsène Heitz, said he had been inspired by images of the Virgin Mary surrounded by a halo of 12 stars.
The amendment was substantially rejected.
The far-right National Front is also hostile to the flag, although it is currently embroiled in an internal dispute about just how Eurosceptic it is.
The party regards the flag as a "supranational" symbol and its leader, Marine Le Pen, demanded that it be removed from the backdrop of one of her television appearances during the presidential election campaign.
The flag, which was adopted by the EU in 1986, first appeared in the French parliament in 2008, while France held the rotating EU presidency.
It has been officially recognised by 16 of the 28 EU's member-states.
Brexit and Catalonia
While at the summit, Macron commented on two of the EU's most important current challenges.
Europe's leaders would send a "message of unity" supporting the Spanish government in its tussle with Catalonia's separatist leaders, he said before meeting Spanish Prime Minister Mariano Rajoy.
And on Brexit, the main subject at the summit, he declared that Britain was still "a long way off" on the financial commitments needed to settle its debts to the EU before quitting the bloc.
While conceding there was "manifest British goodwill", he said that "we have only got half way today" after UK Prime Minister Theresa May refused to enter into details about how much the country would pay.
"Common objectives have been decided on and on the EU 27 side, led by Michel Barnier, we must stick to them," Macron told a press conference. "So I think the problem Theresa May has today is that those who advocated Brexit never explained to the British people what the consequences of that Brexit would be."
Macron himself has vowed to push the EU to reform and has argued for more protection for workers and consumers in negotiating the bloc's free-trade deals.