In the eyes of Syria’s new leaders, the foreign fighters who battled alongside their rebel groups to oust the Assad dictatorship are loyal allies “who have stuck beside the revolution.”

For the United States, many of these fighters conjure images of terrorist groups like the Islamic State.

Thousands of foreigners flocked to Syria to fight in the multi-sided civil war that began in 2011 and lasted nearly 14 years. Some joined rebel groups like the Islamist faction formerly led by Syria’s new president, Ahmed al-Shara, and helped them to unseat President Bashar al-Assad in December.

Now, the foreign fighters who remain in Syria have become a point of contention as the Trump administration takes steps to warm relations with the country. Over the past couple of months, American officials have variously suggested expelling them or excluding them from senior positions in the government and military.

But as Syria’s government rebuilds its military after the devastating war, it has already begun folding some of these foreigners into the army, according to government officials and some of the fighters themselves. The defense, foreign and information ministries did not respond to requests for comment on the matter.

Mr. al-Shara’s rebel group, Hayat Tahrir al-Sham, included many foreign combatants. He now finds himself in the difficult position of trying to balance his loyalties to them with his focus on establishing diplomatic relations with countries that want the fighters either marginalized or gone.