They spoke for nearly an hour in the official papal library in the Vatican’s Apostolic Palace, about twice as long as Francis usually spends with heads of state or government.
A Vatican statement said the two discussed “protection of the environment, migration, and multilateral commitment to conflict prevention and resolution, especially in relation to disarmament”.
They also spoke about prospects for resolving conflicts in the Middle East and Africa and the future of Europe, it said.
“I’ve read this book many times and it has done me good. It is a book that I have always loved very much,” the pope told Macron, 40, who was accompanied in the public parts of the meeting by his wife Brigitte, 65.
Francis gave Macron a medallion depicting Martin of Tours, a 4th century saint who is depicted cutting his cloak in half to give it to a beggar in winter.
“This means the vocation of those who govern is to help the poor. We are all poor,” Francis told Macron as he was giving him the medallion.
As Macron left the library, he and Francis exchanged a two-cheek kiss, another very usually gesture between a pope and a visiting head of state.
The Vatican was expected to issue a statement later on the themes discussed during the private talks.
Two months ago, Macron called for stronger ties between the state and the Catholic Church, a move critics said blurred a line that has kept French government free of religious intervention for generations.
The issue is particularly sensitive in historically Catholic France, where matters of faith and state were separated by law in 1905 and which is now home to Europe’s largest Muslim and Jewish communities.
France’s guiding principles also hold that religious observance is a private matter, for all faiths.
Macron was raised in a non-religious family and was baptized a Roman Catholic at his own request when he was 12.
On Tuesday afternoon Macron was due to be installed as the “First and Only Honorary Canon” of the Rome Basilica of St John’s in Lateran, which is the pope’s cathedral in his capacity as bishop of Rome.
Under a tradition that began in the 15th century when France was a monarchy, French leaders are automatically given the title.