Maher Khalil, 29, even shared sweets with fellow passengers after they kept on enquiring about a small white box and made him open it.
Khalil, who owns a pizza shop in the US, was in Chicago with his friend Anas Ayyad, 28, visiting each other's families and the duo were asked to step aside during the boarding process for returning home because a fellow passenger said he was afraid to fly with them.
"If that person doesn't feel safe, let them take the bus," Khalil told a Southwest Airlines gate agent on Wednesday night after being denied boarding the aircraft.
"We're American citizens just like everybody else," he said as he called the police himself to deal with the unexpected situation.
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The flight was delayed and the two men were ultimately allowed to board after being questioned again by airport security and police. The airline issued a statement acknowledging a brief disagreement with two customers.
While on board, some passengers were very supportive, but others made the flight home outright uncomfortable, Khalil said.
"So I shared my baklava with them."
A second Southwest flight from Chicago to Houston was also delayed on Wednesday when passengers refused to allow six Muslims on the flight. The Muslim passengers had to be rebooked on another flight.
"Safety is our primary focus, and our employees are trained to make decisions to ensure that safety, and to safeguard the security of our crews and customers on every flight," the airline's statement read.