The 87-year-old pontiff landed at Jakarta's Soekarno–Hatta airport on a chartered flight on Tuesday that also carried his entourage and accompanying reporters.
The pope will rest after the overnight flight from Rome before embarking on a rigorous 10-day voyage zigzagging across time zones that will also take him to Papua New Guinea, East Timor and Singapore.
However, the Vatican said the pope would meet on Tuesday with a group of refugees, migrants and sick people at the Vatican residence in Jakarta.
The highlight of Francis' first stop will be his participation on Thursday in an interfaith meeting in Jakarta's iconic Istiqlal mosque with representatives of the six religions that are officially recognised in Indonesia: Islam, Buddhism, Confucianism, Hinduism, Catholicism and Protestantism.
Cardinal Ignatius Suharyo says the pope appreciates Indonesia's interfaith tradition. (AP PHOTO)
The mosque, the largest in Southeast Asia, sits across a piazza from the capital's main Catholic cathedral, Our Lady of Assumption, and the two are so close to each another that the Muslim call to prayer can be heard during mass.
Their proximity is not coincidental, but strongly willed as a symbol of religious freedom and tolerance that is enshrined in Indonesia's Constitution.
The buildings are also linked by an underground 'Tunnel of Friendship' which Francis will visit with the grand imam, Nasaruddin Umar, before they sign a joint declaration.
While Francis will highlight Indonesia's tradition of religious tolerance, the country's image as a moderate Muslim nation has been undermined by flare-ups of intolerance.
In 2021, a militant Islamic couple blew themselves up outside a packed Catholic cathedral on Indonesia's Sulawesi island during a Palm Sunday Mass, injuring at least 20 people.
Even though Catholics make up just three per cent of Indonesia's population, the sheer number of Indonesians - 275 million - makes the archipelago home to the third-largest Christian community in Asia, after the Philippines and China.
As a result, thousands are expected to throng to Francis' events this week, which include a Mass on Thursday afternoon at Jakarta's main stadium expected to draw some 60,000 people.
Care for the environment, conflict resolution and ethically minded economic development are the major themes for the trip.
Francis has made caring for the environment a hallmark of his pontificate and has often used his foreign visits to press his agenda on the need to care for God's creation, prevent exploitation of its natural resources and protect poor people who are bearing the brunt of climate extremes and pollution.
In Jakarta, he will find a metropolis of 11.3 million people choking under grey clouds of air pollution caused by coal-fired power plants, vehicle exhaust, trash burning and factories. Jakarta's air pollution regularly registers eight to nine times above World Health Organisation limits.
Indonesia is important to the Vatican both in terms of Christian-Muslim dialogue and Catholic vocations, since it is home to the world's largest seminary and produces hundreds of priests and other religious workers a year.
"Indonesia is trying to grow in the faith," said Cardinal Ignatius Suharyo Hardjoatmodjo, the archbishop of Jakarta.
He said Francis wanted to express his appreciation for Indonesia's interfaith tradition "and encourage this kind of brotherhood to continue to be maintained and developed".
