"The Christians now live in a terror," said Hussam, a Christian from the nearby town of Saidnaya, who asked not to be identified because he feared for the safety of his family if he was to talk openly.
In the latest major attack on a Christian district, rebels fighting alongside members of the jihadist group Jabhat al-Nusra stormed a government checkpoint at the entrance to the town Sept. 4. The rebel aim was to seize control of a portion of the Damascus-Homs highway, a main route from the capital of Damascus.
The highway is a key supply line for whoever can hold it.
Fearful that the town would be destroyed, hundreds of Christian men from Saidnaya just outside Damascus and elsewhere joined Assad's troops to oust the rebels.
Residents told news media outlets that when rebels entered Maaloula they destroyed precious censors, or incense holders, and Bibles from several churches. Some accused rebels of shelling churches and homes in the town. Others dispute those accounts.
Syrian rebel groups say the Syrian military carried out the shelling of the town and is blaming rebels to stir up trouble.
The small homes of Maaloula wind up a rugged mountain, and once on top one can see a green expanse below of fig trees and vineyards. The town is home to mainly Antiochian Orthodox and Melkite Greek Catholics and Muslims.
One of the oldest surviving monasteries in Syria is here. Called Mar Sarkis, it is the Arabic name for St. Sergius, a Roman soldier executed for his Christian beliefs.
Christians have lived here for centuries. They have largely supported Assad's regime but are increasingly pawns in the propaganda war between the rebels and the regime.
The Syrian government has gone to great lengths to present itself as the sole protector of Christians and other religious minorities, saying it is locked in a battle with terrorists and foreign jihadists bent on destroying the country's secular fabric.
Sama TV, a pro-Assad television station, reported that three Christians were killed by "terrorists" during clashes in Maaloula this month. Its footage impossible to verify showed hundreds of angry mourners at a church in Damascus chanting support for Assad.
Christians hold important roles in Syria's military. And the Assad regime today is heavily dependent on the National Defense Forces groups of local militias armed by the government to keep rebels from entering strategic towns and districts around the country.
Towns such as Saidnaya to the north of Damascus and a cluster of towns west of Homs collectively known as the "Wadi," or valley, have been guarded by armed Christian civilians for months as attacks against the community have increased since the outbreak of the uprising more than two years ago.
But Muslim militias say the idea that the regime is protecting Christians is "foolish," said Joshua Landis, director of the Center of Middle East Studies at Oklahoma University.
"What's happening in Maaloula has happened in one town after the next across Syria. Rebels take a town, the regime responds with overwhelming power and force, lobbing shells, very indiscriminately killing people," Landis said.
Some Syrian Christians say the regime is causing the worst of the attacks to force the Christians to choose sides decisively for the regime. Some even blame the regime for the terrorists being in Syria in the first place.
"I think that the regime is very accomplished in promoting sectarianism," said Osama Edward, 35, a Syrian Christian who runs the Assyrian Network for Human Rights and is currently based in Stockholm. "The incident at Maaloula proves that beyond a reasonable doubt."
Landis says the conflict has exacerbated Christian fears they are being driven out of the Middle East. Christians in Cairo and the West Bank, whose faith predates Islam by centuries, have been leaving their ancient enclaves because of threats and attacks.
"It doesn't take much," Landis said. "Christians were driven out of Anatolia before the first world war. They've been driven out of Iraq. They've been driven out of Palestine/Israel. The Copts have been getting the bad end of the stick in Egypt. The Syrian regime has been taken advantage of Christians feeling their days are numbered."
Christians are still hoping they can avoid taking sides or taking up arms.
"We don't care who is the ruler of this country," said Amar Kassar, a Catholic priest from Qatana, a town west of the capital. Kassar was speaking to Sky News.
Kassar was severely injured by a mortar in a Damascus neighborhood last month.
"We are against the formation of an Islamic state. We want a Syrian secular state for all Syrians," he said.
(Stephen Starr writes for USA Today. Contributing to this report: Abdulrahman al-Masri in Amman, Jordan and Janelle Dumalaon in Berlin.)