Saint Francis' feast day is observed on October 4. A secondary feast in honor of the stigmata received by Saint Francis, celebrated on September 17, was inserted in the General Roman Calendar in 1585 (later than the Tridentine Calendar) and suppressed in 1604, but was restored in 1615. In the New Roman Missal of 1969, it was removed again from the General Calendar, as something of a duplication of the main feast on October 4, and left to the calendars of certain localities and of the Franciscan Order. Wherever the traditional Roman Missal is used, however, the feast of the Stigmata remains in the General Calendar.

Such an incident is alluded to in a scene in the late 13th-century fresco cycle, attributed to Giotto, in the upper basilica at Assisi. It has been suggested that the winged figures atop the columns piercing the roof of the building on the left of the scene are not idols (as Erwin Panofsky had proposed) but are part of the secular iconography of the Sultan, affirming his worldly power which, as the scene demonstrates, is limited even as regards his own "priests" who shun the challenge. Although Bonaventure asserts that the Sultan refused to permit the challenge, subsequent biographies went further, claiming that a fire was actually kindled which Francis unhesitatingly entered without suffering burns. The scene in the fresco adopts a position midway between the two extremes. Since the idea was put forward by the German art Historian, Friedrich Rintelen in 1912, many scholars have expressed doubt that Giotto was the author of the Upper Church frescoes.

On June 18, 1939, Pope Pius XII named Francis a joint Patron Saint of Italy along with Saint Catherine of Siena with the apostolic letter "Licet Commissa". Pope Pius also mentioned the two saints in the laudative discourse he pronounced on May 5, 1949, in the Church of Santa Maria sopra Minerva.

Francis preached the Christian doctrine that the world was created good and beautiful by God but suffers a need for redemption because of human sin. He believed that all creatures should praise God (a Common theme in the Psalms) and the people have a duty to protect and enjoy nature as both the stewards of God's creation and as creatures ourselves. On November 29, 1979, Pope John Paul II declared Saint Francis the Patron Saint of Ecology. Many of the stories that surround the life of Saint Francis say that he had a great love for animals and the environment.

Then during the World Environment Day 1982, John Paul II said that Saint Francis' love and care for creation was a challenge for contemporary Catholics and a reminder "not to behave like dissident predators where nature is concerned, but to assume responsibility for it, taking all care so that everything stays healthy and integrated, so as to offer a welcoming and friendly environment even to those who succeed us." The same Pope wrote on the occasion of the World Day of Peace, January 1, 1990, the saint of Assisi "offers Christians an Example of genuine and deep respect for the integrity of creation ..." He went on to make the point that: "As a friend of the poor who was loved by God's creatures, Saint Francis invited all of creation – animals, plants, natural forces, even Brother Sun and Sister Moon – to give honor and praise to the Lord. The poor man of Assisi gives us striking witness that when we are at peace with God we are better able to devote ourselves to building up that peace with all creation which is inseparable from peace among all peoples."

At his first audience on 16 March 2013, Pope Francis told journalists that he had chosen the name in honor of Saint Francis of Assisi, and had done so because he was especially concerned for the well-being of the poor. He explained that, as it was becoming clear during the conclave voting that he would be elected the new bishop of Rome, the Brazilian Cardinal Cláudio Hummes had embraced him and whispered, "Don't forget the poor", which had made Bergoglio think of the saint. Bergoglio had previously expressed his admiration for St. Francis, explaining that “He brought to Christianity an idea of poverty against the luxury, pride, Vanity of the civil and ecclesiastical powers of the time. He changed history." Bergoglio's selection of his papal name is the first time that a pope has been named Francis.

It has been argued that no one else in history was as dedicated as Francis to imitate the life, and carry out the work of Christ, in Christ’s own way—Francis is sometimes even remembered as alter Christus, ("another Christ"). This is important in understanding Francis' character and his affinity for the Eucharist and respect for the Priests who carried out the sacrament.