Inside a centuries-old monastery atop a mountain in western Syria, a priest swung an incense holder on a chain, led his flock in melodic chants and delivered a timeless sermon on the importance of loving one’s neighbor.

But when the congregation gathered for coffee after the service, their current worries surfaced, about how peaceful Syria’s future would be.

Would the Islamist rebels who ousted the strongman Bashar al-Assad in December ban pork and alcohol, impose modest dress on women or limit Christian worship? Would the new security forces protect Christians from attacks by Muslim extremists?

“Nothing has happened that makes you feel that things are better,” said Mirna Haddad, one of the churchgoers.

Elsewhere in the historic town of Maaloula, its Muslim minority had different concerns. Like their Christian neighbors, they had fled their homes here early in Syria’s 13-year civil war. But unlike the Christians, they had been barred from returning by the Assad regime and a Christian militia it supported.

“The problem is the majority,” meaning the town’s Christians, said Omar Ibrahim Omar, the leader of a new local security committee. He had come home to Maaloula only after Mr. al-Assad’s fall, after being kept out for more than a decade.

“We won’t let that happen again,” he said.

Maaloula, nestled between rugged outcroppings 35 miles northeast of the capital, Damascus, has long embodied Christianity’s ancient roots in Syria and has served as an important piece of the country’s religious mosaic. It is a rare community where locals still speak Aramaic, the language of Jesus, and it boasts a history of coexistence between the two-thirds of its population who are Christians and the other third, who are Sunni Muslims.

But the war that began in 2011 set the two communities on different paths, tearing at Maaloula’s social fabric. Many of the Muslims backed the rebels who fought to topple the regime, while the Christians largely stood by Mr. al-Assad, whom they considered the protector of Syria’s minorities in a Sunni-majority country.

Now, Mr. al-Assad is gone, the town is damaged and its people are struggling to figure out how they might live together once again.

“I want to live with you as brothers,” the priest, the Rev. Fadi Barkil, said in an interview as if speaking to his Muslim neighbors. “If we keep going back to the past, it will never end.”

Christians have been living in Syria since before the Apostle Paul’s conversion on the road to Damascus. Before the civil war, they made up sizable minorities in Damascus, Aleppo and other places, but their numbers have plummeted since. Christians have emigrated to Lebanon and the West to escape the violence and economic hardship that have devastated their communities.

In Maaloula, Father Barkil oversees its Greek Catholic Church and the Monastery of Saints Sergius and Bacchus, whose fourth-century sanctuary is partially hewed from a peak overlooking the town. Next to it are the remains of the Safir Hotel. Once the town’s finest destination for pilgrims and tourists, it was destroyed during the war and is now deserted.

Its terrace overlooks the town, with the domes and crosses of Maaloula’s many churches and the minaret of a mosque rising from amid its simple homes.

The civil war first came to Maaloula when a suicide bomber blew up the main army checkpoint protecting the town in September 2013. Nearly all of its few thousand residents — both Christians and Muslims — fled as fighting erupted, and rebels led by the Nusra Front, an affiliate of Al Qaeda, took control.

The rebels set up bases in the hotel and monastery, which allowed them to fire on government forces below. They kidnapped 13 nuns and three assistants from a Greek Orthodox convent.

The women were later released in a prisoner swap with the government, and the Syrian Army and the Lebanese militant group Hezbollah retook the town in April 2014.

Its Christians returned to find their holy sites damaged.

“When the priests came back after the war, everything was destroyed in the monastery,” Father Barkil said.

The top of its altar had been broken, and shelling had punched holes in its stone walls and in the blue dome over the sanctuary, scattering debris across the wooden pews. Many of its icons were missing, and those that remained had been defaced.

And in what Father Fadi described as a deeply symbolic blow, two giant bells had been stolen from his and another sanctuary, removing their rings from Maaloula’s soundscape.

For the duration of the war, the Syrian army held the town along with a Christian militia that it armed. The Christian sites were restored, although few of the tourists who had once sustained the economy returned.

When the rebels toppled Mr. al-Assad in December, there was little rejoicing among Maaloula’s Christians. The army ran off, leaving the town unprotected, and residents feared that the country’s new Islamist rulers would restrict their religious freedoms.

“What do we want in Maaloula?” Father Barkil asked. “To have a state and security, but we won’t accept for the Muslims to rule us by force.”

Exacerbating their concerns is the fact that the founder of the Nusra Front, the jihadist group that attacked Maaloula in 2013, is now Syria’s president, Ahmed al-Shara.

Father Barkil acknowledged that Mr. al-Shara has said that he cut ties with Al Qaeda and has vowed to serve all of Syria’s people. But the priest called on the new president to reinforce this inclusive message with a visit to Maaloula.

“He can come and say in Maaloula that the Christians are important and that no one can harm them,” Father Barkil said. “But if he never says this, what will happen to us?”

After Mr. al-Assad’s fall, the new authorities sent police officers to secure the town. At the local police station, a few of these new officers — former rebels, all of them Muslims and none of them from Maaloula — were fast asleep in the middle of the day.

Elsewhere, a group of men from a newly formed security committee were crowded around a wood-burning stove, trying to keep warm. They were all Maaloula Muslims, who said that they had fled the fighting in 2013 but that the regime had barred them from coming home because it suspected them of backing the rebels.

Akram Qutayman, 58 and a member of the committee, said that residents of different faiths had lived together peacefully before the war.

“Where I live, I was surrounded by Christians,” he said. “They would celebrate Ramadan with us, as if we were one hand.”

But he accused the local Christian militia of burning the Muslims’ homes while they were away to try to keep them from returning.

“We don’t have houses,” said Mr. Omar, the committee’s head, also noting that the main mosque was still damaged. But he remained hopeful that the tensions would pass and the town would rebuild.

“I expect that there will be reconciliation, and we will live together again,” he said. “We will let the past go.”

Some positive signs have emerged in recent weeks.

The two bells stolen from the churches were returned. They were cleaned, polished and rehung in their belfries during a ceremony last month, their sounds resonating over Maaloula for the first time in 13 years.

“Hanging these bells provided relief to people,” Father Barkil said. “In the end, they are the voice of God.”