The harrowing incident was caught on surveillance camera, and police are hoping the video leads to arrests.
It happened just after 7:30 p.m. on November 29 at the business on Featherbed Lane in the Morris Heights section.
Authorities say two men walked in, displayed weapons and forced their way behind the counter, where the 5-year-old girl was standing.
The video shows her shaking as the men rush past, before she runs behind a display.
One robber grabbed money from the cash register while the other struggled with the 51-year-old owner, Ahlam Alfarah, who is also the girl's mother.
She said she works in the store seven days a week and that her daughter is present more frequently due to schools going remote as a results of the coronavirus pandemic.
"You work hard to give to someone who don't deserve it," she said. "You work hard 14 hours, 16 hours, and then somebody comes and takes it. And maybe he's going to spend it for stupid things."
She spoke to her daughter in Arabic after the suspects entered, so that they wouldn't understand what she was saying.
"I don't have nothing, only a chair," she said. "And I said to my daughter, stay away, don't come here."
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No shots were fired and no serious injuries reported, but the suspects fled with $700.
The business was also robbed just after midnight on November 21, with Alfarah also running the store at the time.
In that incident, the men displayed a firearm and demanded cash before fleeing with $150 in cash.
"He pointed the gun, and I tried to hide here," she said. "And then he jumped, because he's skinny, he jumped, and he made the gun in front of me."
No injuries were reported.
Additionally, just before 6 p.m. on September 27, another violent incident occurred outside the location.
Police say a 63-year-old woman was sitting in her vehicle when an unknown man approached her car, punched her in the face, pulled her from the vehicle and pushed her to the ground.
He then fled in an SUV parked nearby.
The victim suffered pain and bruising to the face and body, and EMS responded but the victim refused medical attention at the scene.
Alfarah is from Yemen and has been in the US for 15 years, and she and her husband have owned their business for six years.
She works in the store seven days a week and says they are now beefing up security.
It is unclear if any of the crimes are connected, but Alfarah said it's possible that one of the suspects from the first robbery could have been part of the second.
She says they were wearing masks, though, and she was not able to give a description. They also didn't say much, she said, so couldn't be sure if they were the same men.
Anyone with information in any of them is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
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