The 87-year-old pontiff was pressed by high-profile figures at three of the five major events on his three-day visit in unusual and sometimes fierce language for a papal trip.
In a meeting with Belgian dignitaries on Friday, both King Philippe and Prime Minister Alexander De Croo called for more concrete action to help survivors of abuse by Catholic clergy.
And in later events at two Catholic universities, officials denounced his stance on the role of women in the church and society.
Francis did not specifically mention the criticisms at his last event in Belgium on Sunday, a celebration of mass at Brussels' King Baudouin football stadium.
The Belgian tour was Francis's 46th trip abroad since being elected pope in 2013. (AP PHOTO)
But the Pope did add to the prepared text for his sermon and made a strong condemnation of Catholic clergy abuse.
"There is no place for abuse," the pontiff said, drawing scattered applause from the estimated 37,000 attendees on Sunday.
"There is no place for the cover-up of abuse.
"I ask everyone, do not cover up abuse. I ask bishops, do not cover up abuse".
The Belgian tour, which started with a one-day visit to nearby Luxembourg, was Francis's 46th trip abroad since being elected pope in March 2013.
The visit was meant to focus on the 600th anniversary of the two Catholic universities.
Francis has also faced such criticism on previous tours, especially on the issue of clergy sexual abuse.
On a trip to Chile in 2018 groups of demonstrators protested outside his events and Catholic churches were attacked before his visit.
But Francis, leader of the world's 1.4 billion Catholics, is not usually confronted directly in public by political leaders or Catholic officials organising his events.
Professors and students at UCLouvain, where Francis gave a talk on Saturday afternoon, issued a press release moments after the pope had finished speaking, saying they wanted to express their "disapproval" of his views.
The Pope's speech at the university largely called for global action on climate change, but he also responded to a letter to him from students and professors that had asked about the Catholic Church's teaching on women.
Francis emphasised that the church, which bans ordination of women to the priesthood, was not run like a corporation.
He described women as having "a fertile welcome, care (and) vital devotion".
The Vatican did not respond to the university's statement.
Francis apologised on Friday for sexual abuse by Catholic clergy in Belgium, saying the church must "be ashamed and ask forgiveness".
He also held a two-hour meeting with a group of survivors, who pressed him to provide better financial compensation for victims.
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