As the convoy of Muslims left the besieged neighborhood, villagers lined the roadside for one last glimpse of their fleeing countrymen. Some of the Muslims packed into the open-air trucks met the villagers’ stares with waves. Others returned only stony gazes, or made rude gestures.

It was a final exchange between the 1,300 Muslims sheltering in a neighborhood on the northern flank of the Central African Republic’s capital of Bangui and the Christian countrymen who had turned against them, prompting their flight to the country’s north.

Already, mobs were at work in the streets they once called home, taking what they could and doing their best to make sure the Muslims never came back.

“Allahu Akbar!” yelled Raphaela Nado mockingly, as she strode past the neighborhood’s mosque, which had its doors and windows ripped off by looters, some of them wielding knives and clad with colorful good-luck charms. Two men were busy hauling out the minbar, a type of pulpit used by the imam, when Congolese troops intervened to stop the mosque’s destruction.

After months of atrocities blamed on a Muslim-dominated former government that Ms. Nado says forced her into a displaced persons’ camp, she sees the mosque’s sacking as a moment of comeuppance and liberation. “We are getting our freedom,” she says.

The evacuation of Bangui's PK12 neighborhood last Sunday, organized by aid groups, is symbolic of what is playing out across the CAR, where, since January, Muslims have been targeted by Christian-dominated militias. Once-diverse Bangui has grown closer to being completely "cleansed" of Muslims, and thousands are leaving their homes for safer spots in the country or heading to neighboring Chad or Cameroon. But their flight is bringing worries that the mass displacement could only further destabilize the CAR, and perhaps play into the hands of jihadi groups looking for new recruits.

“We have an entire generation of young Muslims men who have lost everything and are extremely angry,” says Peter Bouckaert, emergencies director for Human Rights Watch. “This will not be the last round of fighting.”

The Séléka government’s ouster in January is seen as the start of intense violence targeted at Muslim communities across this country of 4.6 million.

The Séléka, a group of predominantly Muslim northern rebels, came to power by overrunning the capital and sending then-President François Bozizé packing. But their president, Michel Djotodia, did little governing during his 10 months in office. Rather, the Séléka fighters murdered alleged Bozizé sympathizers and razed villages across the country.

By December, self-defense forces called the anti-Balaka, which were mostly Christian, had mobilized to check the rampage. By the time neighboring countries pressured Mr. Djotodia to resign in January, many anti-Balaka had decided that all Muslims, not just the Séléka, had to go.

Mobs wrecked mosques in Bangui, murdered Muslims in the countryside, and drove thousands into enclaves like Bangui’s PK12 and PK5 neighborhoods. The latter is now the sole haven for Muslims in Bangui.

But despite the presence of foreign peacekeepers from France and the African Union, the enclaves are by no means secure. The besieged communities continue to be flashpoints both for anti-Balaka incursions and retaliations by armed Muslims.

In their last days in PK12, most Muslims just wanted to go.

“They killed all our parents, all our children,” says Salie Hassan, a resident waiting for evacuation. “We can’t live here.”

But the refugee camps to which many are headed may breed another problem: a receptive audience for jihadi groups of jobless young men. Cameroon is home to more than 175,000 refugees from the fighting, and the Nigerian extremist group Boko Haram has already made incursions into Cameroon's north.

“Certainly jihadi groups will look at the Central African Republic with great interest,” Mr. Bouckaert says. While he says the conflict in the CAR is driven more by politics than religion, the country’s long history of weak governance makes it an attractive place for Islamists to base themselves.

On the streets of PK12, the pillaging took on a decidedly religious tinge. Women prostrated themselves scornfully on the street, yelling “Allahu Akbar,” while young men spray-painted “youth center” on the outside of the mosque.

Others settled for merely trashing houses and making off with plywood or aluminum siding.

“They are savage, they destroy our houses. We can’t live with them,” says Tcholongba Gauthier, one of the looters, referring to the former Muslim residents. “That’s why we destroy theirs.”

Maxime Gbemedengo walked amid the looters with a knife strapped to his back and a smile on his face. The commander of the local anti-Balaka, Mr. Gbemedengo lost his house and nearly his life to Séléka fighters. He was happy to see the Muslims gone; as far as he was concerned, there was no place for them in the country anymore.

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“We need to stop the looting,” Mr. Gbemedengo declared.

But his intention was not to safeguard the Muslims’ property. Instead, he aimed to make sure that the Christians who would be moving into the neighborhood have somewhere to sleep.