It was a single mouse that was recorded on Thursday by a customer standing in line for the bakery's trendy pastries.
By the end of the day on Friday, city health inspectors shut the place down, citing what they call a "severe infestation".
"The pastries are delicious, so I can't blame the mice, there's a reason why they're here," said customer Justin Holmes.
Dominique Ansel is a French pastry chef who became an overnight hit when he fried up a croissant in the shape of a donut, and called it a cronut. He later trademarked the name. Tourists stand in line for hours to buy one.
Nicole Ong once tried a knockoff cronut at home in Singapore.
"It's okay, I don't like cronuts anyway," says Ong, who came to Dominique Ansel Bakery just to check out the hype.
In its last inspection six months ago, the bakery did get an A, despite what the Department of Health at the time called "evidence of mice". The facility, it said "not vermin proof".
After viewing the video, inspectors found tiny holes and 300 mouse droppings, so they pulled the plug on the business until the bakery can seal up the holes and hire an exterminator.
On Friday, a worker returned from the hardware store with cement and other supplies. Meanwhile, regular customers don't seem all that upset. A neighbor even suggested Ansel had been targeted because of his fame.