The pontiff opened his second and final day on the Mediterranean island by visiting the holy grotto of Saint Paul in Rabat — where the disciple stayed after being shipwrecked on his way to Rome in 60 AD — before leading a mass for a crowd of 20,000.
In a symbolic likening of the apostle’s need for a safe haven with that of refugees, the Pope used his visit to drive home his customary call for Europeans to show better treatment of arrivals in their respective countries.
He recalled how Saint Paul and his fellow travellers were welcomed, even though "no one knew their names, their place of birth or their social status".
He called on God to "help us to recognise from afar those in need, struggling amidst the waves of the sea, dashed against the reefs of unknown shores" and grant that "our compassion be more than empty words".
Pope Francis went on to hold an open-air mass in Floriana, near the capital Valletta, before visiting a migrant centre in the afternoon that will soon host refugees fleeing the Ukraine war.
Russia's invasion of Ukraine has overshadowed the Pope's first trip to Catholic-majority Malta, a visit delayed by two years due to the pandemic. The short trip has been taxing for the pontiff, 85, who is suffering from strained knee ligaments.
On Saturday, the pope had given a warning that "some potentate, sadly caught up in anachronistic claims of nationalist interests, is provoking and fomenting conflicts" in a thinly veiled swipe at Russian President Vladimir Putin.
He told reporters that a papal visit to Ukraine's capital was "on the table" but gave no further details.
In a hard-hitting speech in Malta's presidential palace on the first day of his trip, the pope reminded the island nation of its status as a "safe harbour".
"The growing migration emergency — here we can think of the refugees from war-torn Ukraine — calls for a broad-based and shared response," he said.
The war has sparked the worst refugee crisis in Europe since the Second World War, with more than 4 million people having fled Ukraine since the invasion began, latest United Nations' figures suggest.
The need to welcome and embrace people fleeing conflict, poverty or the effects of climate change has been a leading theme of the Pope's nine-year tenure.
Malta has long been at the heart of the European refugee policy debate. The country of 444,000 people is frequently criticised by humanitarian groups for refusing to allow rescue ships to dock.
The government argues it has one of the European Union’s highest rates in processing first-time asylum applications and says other, bigger European countries should do more to shoulder the burden.
While thanking Malta for its welcome of newcomers, Pope Francis criticised the EU policy that trains the Libyan coastguard to return smuggled migrants back to shore.
Human rights groups have documented gross abuse at the Libyan detention centres where the returned migrants are then often housed.
“Civilised countries cannot approve for their own interest sordid agreements with criminals who enslave other human beings,” he said.
The pontiff is wrapping up his trip with a visit to a shelter run by volunteers that can house 50 migrants and provide them with educational and medical services.
Most of its occupants come from Somalia, Eritrea and Sudan and made the perilous Mediterranean crossing from Libya.
Staff at the John XXIII Peace Lab, a centre inspired by the pope of that name, are preparing for the arrival of Ukrainian refugees.
Run for the past five decades by a Franciscan friar, now 91, it already hosts 55 young men from across Africa who arrived in Malta without legal papers.