With Europe reeling from a series of terror attacks targeting civilians, Poland will deploy over 20,000 policemen and has temporarily restored border checks with EU neighbours.
Though World Youth Day organisers expected nearly two million pilgrims, only around 400,000 have officially registered.
The 79-year-old Argentine pontiff, a son of Italian immigrants, has chosen a theme of mercy for the 2016 edition of the faith extravaganza, dubbed "the Catholic Woodstock".
Francis will meet Holocaust survivors at the former Nazi German death camp Auschwitz, and lead prayers for its 1.1 million mostly Jewish victims with Poland's chief rabbi Michael Schudrich, who has called the site "the worst place in the world".
Much of it will take place in the southern city of Krakow, whose most famous resident was John Paul II.
The late Polish pope and saint, who launched the Catholic festival in 1986, is still considered The Pope by many in his homeland.
Given the theme of "blessed are the merciful, for they will receive mercy," Europe's record migrant crisis is expected to figure high on the agenda.
"Refugees? The pope will say something on that," Archbishop Celestino Migliore, the Vatican ambassador to Poland, told AFP.
The pontiff's position is clear. He has called on every European parish to take in one refugee family - and he practises what he preaches.
Francis flew 12 Syrian Muslim asylum seekers back to the Vatican aboard his plane during an April trip to the Greek island of Lesbos, a migrant hotspot.
"I didn't make a choice between Christians and Muslims. All refugees are children of God," he said at the time.
When his right-hand man Pietro Parolin visited Poland that same month, he called on Catholics to "open Church doors, including to refugees".
But Polish Prime Minister Beata Szydlo and her right-wing government, all loyal Catholics, are loathe to welcome refugees for security reasons. A good chunk of the public agrees.
Even the country's bishops were not fired up about the idea, but just four days ahead of the pope's arrival they appear to have had a change of heart.
They joined other Christian denominations in Poland on Saturday to urge charity towards refugees and recalled the Biblical passage where Jesus was also a child refugee as his family fled the murderous tyrant, King Herod.
At the same time, a spokesman for the Polish episcopate highlighted the "great fears" Poles have about the possible influx of refugees into their ethnically homogenous land.
Francis's trip to Krakow will see him retrace John Paul II's steps, such as when he waves on Wednesday evening from the first floor window of the archbishop's residence as Karol Wojtyla once did.
But he will also do his own thing, opting for example to take the tram to Blonia meadow in the city centre for Thursday's welcome ceremony.
While awaiting his arrival, tens of thousands of youths from across the world have flocked to Polish dioceses, welcomed by an army of volunteers and host families.
A diverse programme of events is on offer for them: from concerts, break-dancing, football matches and kayaking - one of John Paul II's favourite pastimes - to preparing meals for the homeless and cleaning the houses of the blind.
The grand finale will include a papal vigil in a meadow in the village of Brzegi, outside Krakow, on July 30.
After a night spent sleeping under the stars, the youths will take part in a final mass during which Francis is expected to call on them to share the message of mercy back home.