Members of the Salafi movement — an ultra-conservative current within the Sunni branch of Islam — have been based in the Gaza Strip for the past decade or so, but in recent months their presence has spread to the West Bank. While most Salafis are non-violent, the extremist fringes have a strong jihadist element that borrows from al-Qaeda's ideology, as can be witnessed in Gaza,  Syria and the Sinai, where in recent years such groups have thrived. The stated endgame of the extremists is to establish an Islamic caliphate — and Christians, Jews and others are considered infidels.

In Bethlehem, residents talk about an increasingly antagonistic climate between faiths. Just weeks prior to the Pope's visit, a proselytising group of Muslims stood near the entrance of the Church of the Nativity, handing out copies of the Koran in multiple languages, and telling people on their way to the church to pray to Allah instead. "It was insulting. I feel like I don't live in a Christian place any more," says Samir, adding that such events are happening more and more often.

A few days after the incident outside the Church of the Nativity, he describes celebrating the feast of St George in another church a few miles outside Bethlehem when a violent brawl between Christian and Muslim worshippers broke out. Stones were thrown, and a video of the event shows people running away in fear. Samir said the event was terrifying. "They will throw us out of our own country."

About 60 miles away in northern Israel, a must-stop site for Christian pilgrims is the Basilica of the Annunciation in Nazareth, the largest church in the Middle East. Surrounded by stained-glass windows and mosaics from all over the world, the airy nave of the church leads you eventually down a dimly-lit stairway to a sunken enclosure which marks the spot where Mary was famously visited by  the Angel Gabriel, who told her that she was expecting "the Son of God".

Yet to step inside the church, worshippers must pass large posters hung outside, decorated with a warning triangle and stating: "Allah is the one and only God". Rejecting Jesus, the signs go on to proclaim that "his holiness is far above having a son".

No one knows exactly who is responsible for the posters. "Some tried to take the signs down and burn them several times already," explains Leon Barra, a 30-year-old who has lived in Nazareth all his life. "But two weeks later they were back up."

"We wrote to the Pope, asking him to come here because we need his support," says one shopkeeper selling jewellery at a nearby stall. "He replied saying that he did not have enough time, but that the time to visit Nazareth will come."

Christians in Israel are a minority within a minority. Approximately 20 per cent of Israel's population of 8 million are Arabs — of whom ten percent are Christians. Although the number of Christians living in Israel between 1949 and 2013 has more than quadrupled, according to Israel's Central Bureau of Statistics, the overall Christian share of Israel's population has decreased over the years because of migration and low birthrates — from 2.5 per cent in 1950 to 1.6 per cent now.

In the winding alleys of Nazareth's old city market, several Christian shopkeepers confide on condition of anonymity that criminal gangs subject some of the local businesses to intimidation and death threats if they do not pay monthly protection money.