New Yorker Sarab Al-Jijakli has long lived by a simple rule: food is just that much better in New Jersey. The 37-year-old had been an advertising executive by day and gourmet by night for many years. But it all changed when the war between President Bashar Al-Assad and rebel forces erupted in his native Syria.

Since then, the Brooklyn resident has stopped going to Sultan, a cozy Middle Eastern restaurant with a lavish menu in Clifton, New Jersey. No more fattoush sprinkled with crispy triangles of fried pita, and goodbye eras naana, a grilled meat cooked with mint. A sacrifice, certainly, but one Al-Jijakli does not regret.

That's because the restaurant, like many other establishments across the country, has become one of the many battlegrounds where the conflict has taken a domestic foothold. Founded by a pair of Syrian American friends in 1995, Sultan became mired in controversy, its mezze a guilty pleasure, when in the first months of the conflict in 2011 the pair were rumored to have quarreled, one partner in favor of Assad, the other against. When the latter walked out, leaving the pro-Assad partner in charge, opposition sympathizers like Al-Jijakli began boycotting the restaurant.

At a time when Syria is torn apart by a conflict that has divided its population along sectarian lines, Syrians in the United States have also been waging a battle along imaginary frontlines that criss-cross the everyday institutions that once brought them together. Although the war rages thousands of kilometers away and such violence here is unthinkable, Syrian Americans have still mobilized to fight a mirroring conflict that consumes personal and professional life.

Syrians have never had a big presence in the United States, but the Syrian American diaspora has trickled into the country at a regular pace since the first important wave of immigrants arrived in the late 19th century. In 2005, there were 154,560 Syrians in America, according to the US census bureau – a drop in the US melting pot that finds its collective identity in its restaurants, temples and associations. Or at least it did, until the Syrian homeland spiralled into a conflict that has seen bloodletting on an unprecedented scale. The United Nations estimates that some 70,000 Syrians have perished so far since the beginning of the Syrian civil war in March 2011.

Syrian American men have tea at a terrasse on Main Street in the town of Paterson, New Jersey. Photograph: Sebastien Malo

Mohamed Khairullah, too, frequented Sultan Restaurant, until he learned about the political convictions of its owner. He now shuns it. Khairullah traveled with his family from Aleppo, Syria, to Prospect Park, a small town in New Jersey, at the age of five, and grew up to become the small town's mayor, a position he has held since 2007. Throughout the years, he has kept a close connection with his cousins, aunts and uncles in Aleppo, a city of two million that was transformed into an urban warzone last summer and has yet to recover. When he was invited by a charity group to attend a function at Sultan, Kahirulla's took a stance. "I flat out said I wouldn't attend." The group changed the venue. (The owner of Sultan Restaurant turned down a request for comment.)

Pro-Assad Syrian businesses are not the only ones to be targeted. Syrian Americans supporting the revolution have also been avoiding small businesses they deem to be uncooperative with revolution activists. In the town of Paterson, New Jersey, some like Khairullah have declared two supermarkets owned by Syrian immigrants and frequented by the diaspora, Nouri Brothers and Fattal, a no man's land for pro-revolutionaries. The owners of the two supermarkets specialized in Middle Eastern products had refused to pin to their billboards pro-revolution posters that advertised fundraising efforts or protests in the early days of the revolution. "When we asked them to post something that has to do with the revolution, they would refuse," he said.

Albert Nouri, a co-owner of Nouri Brothers, said he was unaware of the informal boycott, and that he wanted to stay clear of any discussion on the Syrian conflict. Nouri was born in Syria and planted his roots in the United States more than three decades ago, though he still has distant family members in his home country. "Anybody who talks to me here about politics I say 'Please, no, this place is not for politics,'" he said. "We sell cheese and olive and bread. This is a place to do business, not politics."

Still, Kahirulla said that kind of attitude was sufficient ground for boycott. "The wishy washiness in itself, with the amount of killing that's going on, it forces us to take a stance," he said. "As silly as this might sound, it's important to us now because it's our families that are getting killed, and anybody who stands with the killer is not someone we want to support financially."

Associations have also been affected. Al-Jijakli heads the Network of Arab-American Professionals, a non-profit with chapters across the country. As president, he has pushed for the organization to take a stance in favor of the anti-Assad opposition. The group, with about 2,000 members in New York and New Jersey, has sent hundreds of thousands of dollars worth of humanitarian aid to towns and cities under rebel control in Syria. But the move also sent his organization temporarily spinning out of control, as members disagreed over which side of the conflict to root for. When at its annual street festival the group raised the green-white-black Syrian flag of independence instead of red-white-black one which the current Syrian government uses, some pro-Assad members expressed their irritation.

A pedestrian walks alongside Nouri Brothers supermarket, in Paterson, New Jersey. The business is one of the many establishments that pro-revolution Syrian Americans boycott. Photograph: Sebastien Malo

"When the revolution hit, pretty much across all Syrian American organizations a couple of things happened," he said. "One was, for the most part, the organizations pretty much had to make a choice and internally, there were squabbles which kicked out the pro-Assad leadership."

That polarization does not surprise University of Oklahoma professor and Syria expert Joshua Landis, who says it merely reflects the sectarian divide in Syria. The Syrian civil war is widely read as a conflict between the majority Sunni Muslim community and a patchwork of religious minorities – among them Alawite Muslims, Christians and Druze Muslims. "Sectarian identity is a large part of Syrians, and it gets imported to America," he said. "Anti-Assad is just a code word for Sunni, for people who don't like to speak about it."

But some Syrians say the phenomenon has also resulted in the rebirth of their community. In Syria and in the US, without the usual heavy involvement of the Syrian government – known for its authoritarianism – in civil society, genuine grassroots organizations have grown for the first time in decades. Zaher Sahloul, a Chicago-based 47-year-old physician specializing in pulmonary disease, is another anti-Assad activist and the volunteer director of the Syrian American Medical Society.

The group went through a lengthy period of internal discord before taking a pro-revolution stance; members were uneasy when in the months following the beginning of the conflict the organization ignored it. "Our people were restless," he said.

When the organization finally sent medical doctors to Syria and bordering countries to treat civilians, two board members stepped down. "One of them is known to be a friend of one of the very close circles of Assad – the cousin of Assad. The other person, his family owns a hospital that is frequented by government fighters," Sahloul said. But after the initial backlash, participation in the organization spiked, surging to 500 members from an original 140. "Of course, people who thought sending medical relief was a political statement left the organization," he said.

At the Nouri Brothers supermarket, Albert Nouri said he had no doubt customers would see past the boycott. "We've been here for a long time, we know what we're doing in the business."

His boycotter, Kahirulla, agreed that he could foresee the day when the boycott would end and business would resume as usual. Resuming life as usual, however, could take longer. "We have a long way to heal, because people have put their trenches in the ground," he said.

• This article was amended on 14 August 2013 to clarify that the Network of Arab-American Professionals membership figures relate only to the New York/New Jersey area. The president of the NAAP also wishes to clarify that funds sent to Syria went through US-based relief non-profits that work with refugees and internally displaced populations.