Protests have broken out in Bethlehem as Palestinians rallied against the Greek Orthodox patriarch, accusing him of selling church land to Israelis.
Angry protesters on Saturday threw eggs and attacked the convoy of Theophilos III as it made its way its way to Bethlehem's Manger Square in the occupied West Bank.
The patriarch was visiting the Church of the Nativity for services marking the Orthodox Christmas Eve. Many Orthodox Christians celebrate the birth of Jesus Christ on January 7.
The patriarch has been at the centre of public anger after recent news reports alleged that the church leader had been involved in property sales to foreign tax havens, and those properties may end up in the hands of Israeli businesses.
A protest calling for the removal of Theophilos III was also held in September following the publication of reports claiming that he had colluded with a settler organisation.
The settler group, Ateret Cohanim, has been working for decades to evict Palestinians from their homes and shops in the city, including around important holy sites such as the al-Aqsa Mosque compound.
Speaking to Al Jazeera, representatives of the Greek Orthodox Church of Jerusalem denied the reported allegations.
"We did not, as they claim, sell our land to the Israeli occupation," said Father Issa Musleh.
"Those are old deals the patriarch wants to rectify and clarify, because all those old deals are detrimental to the rights of the patriarchate and its congregation."
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Al Jazeera's Mohammed Jamjoom, reporting from Bethlehem, described Saturday's scenes as "unprecedented" and "dramatic".
"There have been protests before, but not at this level. There were eggs being hurled at the convoy, people sitting in the middle of streets. It really underscores how angry people are about these reports," he said.
"Local officials also gave him a cold shoulder when they refused to welcome him to the square," added Jamjoom.
The Orthodox Church is reportedly the second-biggest landowner in East Jerusalem, and many Palestinians think the sales of East Jerusalem land to Israelis will endanger the future of East Jerusalem as the capital of a future Palestinian state.
However, the land sales have triggered a broader campaign demanding an end to the church's dominance by Greek-born clergy.
Past protests have called for Palestinian clerics to take over the patriarchate.
"Our demands are clear and simple," Aghlab Khoury, a member of the Orthodox Central Council, told Al Jazeera at the Bethlehem protest.
"We want the patriarch to resign; we want reform to the patriarchate; assign a legal committee to evaluate the situation in the patriarchate; and appraise the existing property."
The protests came one month after US President Donald Trump officially recognised Jerusalem as the capital of Israel and said he would start a process to move the US embassy from Tel Aviv to the holy city.
That decision led to massive protests in the occupied Palestinian territories and major rallies in support of the Palestinians across the Muslim world.
A majority of UN member also heavily criticised Trump's announcement, declaring his Jerusalem move "null and void".
Al Jazeera's Jamjoom said the events of the past month reinforced the sombre mood in Bethlehem and overshadowed the traditional Christmas festivities.
"I spoke to a man who has been coming here for decades to celebrate, and he said he had never seen it this empty," said Jamjoom.
"In the past, Muslims would be out here, Christians would be out here. The courtyard would be full of children. But up until now, it has been very empty outside of the Church of the Nativity," he added.
"It is one more thing that highlights the hopelessness that Palestinian Christians are feeling right now, in a period where they should be feeling peaceful, festive and hopeful."