The Williamsburg shop known for their Instagram-friendly “Rainbow Bagels” has been shut down for owing more than $100,000 in unpaid taxes.

Signs posted on The Bagel Store — the alleged home of the “Original Rainbow Bagel” — on Metropolitan Ave near Graham Ave say it’s been “seized for nonpayment of taxes” by the New York State Department of Taxation and Finance.

The popular baked-good shop was issued three warrants May 23 for a combined sum of $128,224.53, records show.

On their Instagram account, the cash-only eatery said it “ran into a major operations issue” and that they would reopen “as soon as possible.”

“Thank you to everyone for giving us positive vibes while we work towards a solution to our closure. And for all those people who are negative in all this is for you,” it posted, with an emoji of a fist with middle finger salute.

Owner and baker Scot Rossillo confirmed the reason behind the closure to Gothamist, which first reported Thursday that the shop had shuttered.

“Yes it is true, we’ve had some difficulties lately with the tax department, but then again I don’t know any business that has been in business for a long time that has not had their share of issues with any governmental agency,” Rossillo said.

Rossillo has been hawking the clownish-looking bagels since the mid-1990s, but it took a viral 2016 video for them to blow up and prompt nearly 2-hour long waits. He didn’t return a call from The Post Thursday.

Some locals were shocked over the closure.

“I would never have guessed they had so much debt. I initially thought they closed because of their horrible AC,” said 23-year-old Bianca Ulics, who was at the shop as recently as last week.

Cono Mazza, 62, who has lived two blocks from the store all his life said he “used to go there all the time.”

“I’m really surprised they closed,” he said. But, he added: “When you deal only in cash, it’s easy to rob the government. But the IRS is smart. They’ll get you. They’ll pay attention and it’ll catch up.”

The former deli owner said “the neighborhood will definitely miss out” while the store is closed.

“But my wife thinks the neighborhood is a little too commercial,” Mazza said. “So maybe this will tone it down a little. I’m ready to move whenever she says.”