The employee got into an argument - or attempted to intervene in a dispute - with a woman over food inside the eatery at around 7 p.m. Monday.
Officials say the 40-year-old customer complained her fries were cold to the victim who was working behind the counter.
As the argument escalated, she called her 20-year-old son on FaceTime who went to the restaurant to confront the worker himself.
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Police say he saw the employee outside and pulled out a handgun and shot the victim once.
He was struck in the neck and rushed to Brookdale University Hospital, where he is in critical condition.
The woman's 20-year-old son was taken into custody at the scene and is being questioned.
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McDonald's worker shot in face during dispute in NYC
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The victim does not appear to have any prior connection to the suspect or his mother.
The shooting has similarities to several recent incidents of violence against fast food restaurant workers.
In May, a McDonald's worker was stabbed multiple times defending other employees from an unruly customer in East Harlem.
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And in January, 19-year-old Kristal Bayron-Nieves was fatally shot during an armed robbery inside a Burger King in East Harlem.
At least one resident Eyewitness News spoke with said customers often take fast food workers for granted, and need to do better.
"Let's just all be kinder to each other," said Lilo Mitchell.
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