The yearlong uprising against Syrian President Bashar al-Assad has been followed by the appearance of armed militias, some loyal to the regime and others made up of former Syrian army members who now carry out attacks on government troops.
Those at the monastery said it was impossible to determine the identity of their assailants.
"There were many contradictory elements," Sister Dina, a Catholic nun from Homs who works at the monastery, told Catholic News Service. "They asked for money and weapons, but at the same time they didn't steal anything and they didn't cause much damage."
In a telephone interview, Sister Dina, who asked that her last name not be used, said she was meditating in the monastery's chapel when the intruders burst in, about 7:30 p.m.
"Three of the men charged in -- one blocked my way with a gun," she told Catholic News Service. "I asked them what they wanted and told them this is a place of worship that should be respected.
"One man said, 'Don't worry, we won't hurt you,'" she continued, describing "professional" assailants who appeared "used to carrying weapons."
"They broke all our means of communication, our computer, our phones, then they told us to stay in the chapel for one hour as they left," she said.
Local authorities told the monastery that nearby villages had been struck by similar attacks, with an armed group stealing from homes and shops.
The monastery's superior, Italian Jesuit Father Paolo Dall'Oglio, was reportedly in the Syrian capital, Damascus, when the attack took place. Sister Dina said March 2 that he was due to return to Mar Musa within the next few days.
In December, Father Dall'Oglio, who once said he developed Mar Musa "to build harmony around a religious fault line," was reportedly asked to leave Syria after he told a Catholic newspaper the country could no longer live under a "totalitarian dictatorship."
As Sister Dina gave her account of the attack, government forces were claiming victory in the formerly rebel-held district of Baba Amr in Homs.
The central Syrian city is home to a sizeable Christian minority, the majority Greek and Syrian Orthodox.
"My family is still there, we talk on the phone every day," said Sister Dina, adding that her relatives have escaped the worst of the onslaught.
Christians are said to make up around 10 percent of Syria's roughly 22.5 million population. Their participation in the country's uprising has been limited, say activists, citing Christian fears of a future Islamist government.
In Mar Musa, Sister Dina said, monastic life was slowly returning to normal, even as Syria's uprising continued.
"It's been snowing for three days so we feel more protected here in the mountains," she said.