Speaking to journalists in English aboard his flight to Angola for the third leg of his 10-day Africa tour, the first US-born pontiff said comments he made two days earlier in Cameroon decrying that the world was being "ravaged by a handful of tyrants" were not aimed at Trump.
That speech, said Leo, "was prepared two weeks ago, well before the president ever commented on myself and on the message of peace that I am promoting".
"As it happens, it was looked at as if I was trying to debate the president, which is not in my interest at all," the pontiff said on Saturday.
The Pope's remarks about tyrants were made to a peace meeting in the city of Bamenda, Cameroon - the epicentre of a separatist conflict that has been raging in the Anglophone region of the country for nearly a decade.
A week ago as Leo prepared to embark on his tour, Trump called him "weak on crime, and terrible for foreign policy" in a post on Truth Social.
The Pope said on Saturday his preaching is not directed at Trump but reflects the broader Gospel message of peace.
"There's been a certain narrative that has not been accurate in all of its aspects but because of the political situation created when, on the first day of the trip, the president of the United States made some comments about myself," the pontiff said.
"Much of what has been written since then has been more commentary on commentary, trying to interpret what has been said."
Leo has issued consistent calls for peace and dialogue, and has denounced the use of religious justification for war.
Specifically, he called Trump's threat in an online post to annihilate Iranian civilisation "truly unacceptable".
The Vatican has stressed that when Leo preaches about peace he is referring to all wars ravaging the planet and not just the Iran conflict.
Looking ahead, the Pope said that he would continue preaching the Gospel.
"I primarily come to Africa as a pastor, as the head of the Catholic Church to be with, to celebrate with, to encourage and accompany all the Catholics throughout Africa," he said.
He drew attention to some upcoming liturgical readings about what it means to be Christian and to follow Christ, promote fraternity and brotherhood "but also looking for ways to promote justice in our world, promote peace in our world," he said.
with AP