The Dominique Ansel Bakery in Soho, best known for its croissant-donut hybrid, made headlines last week when cell phone video went viral, showing a mouse scurrying behind the counter.
Health inspectors ordered the shop closed until holes were patched.
Monday, a message on the shop's Facebook page, said "We have completely fortified our facilities with a full reconstruction and re-cementing, taking every issue seriously."
At the bakery on Friday night, workers were trying to paper over their windows when Eyewitness News turned on the camera lights. At which point, for whatever reason, they ripped the paper down, and scurried away - kind of like mice.
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".
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.
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 could seal up the holes and hire an exterminator.