The beloved 124-year-old Brooklyn bakery that suddenly shuttered last month, saying its owner wanted to spend more time with family, actually had its state license yanked over stomach-churning violations.

James Caputo, proprietor of Caputo’s Bake Shop in Carroll Gardens, told local news outlets in April that he decided to suddenly close up shop to spend more time with family.

He noted that he couldn’t shell out the dough needed to fix his Italian-made Logiudice commercial bread oven, either – and didn’t want to pass the business on to someone outside the family to keep it alive.

It turns out the bakery also had been plagued with state health-code violations ranging from mold to mouse droppings for more than a year, according to a Post analysis of records — with the historic bread shop’s license revoked in January.

“I just honestly didn’t want to be cast in that light,” Caputo, 54, told The Post when asked why he didn’t mention the Department of Agriculture and Markets violations when talking to the press about closing.

“I think anybody would have felt that way.”

Caputo said he was confident that a re-inspection of his shop would have quickly returned his coveted license, and he blamed serious medical issues, mental stress of the job and the century-old bakery’s wear-and-tear as reasons to hang up his apron and not re-apply for the state’s approval.

“I had done this for 25 years, and it’s been a rough 25 years,” he said. “My health had been deteriorating over the years, and it wasn’t the physicality of the job: It was the mental stress, 24 hours a day, seven days a week, 365 days a year.”

On Monday morning, April 27, he taped his farewell letter on the bakery’s door.

“It is with immense sadness that I am writing to tell you the flame in our oven has been lit for the last time,” he wrote, adding, “Last night was the last night of production.”

Mourners have since turned the shop’s doorstep into a shrine, taping signs of heartfelt gratitude on its windows.

“Please, please change your mind!!” someone urged.

Nearby Sacred Hearts & St. Stephen Catholic Parish wrote on Instagram, “For generations, it was more than a bakery.

“Sunday mornings after church, holidays, family traditions — you could taste the love and history in everything they made.”

Caputo told The Post, “Everybody who told me how great we were, how much they loved me.

“I always wanted my bread to be better. I was never happy with the product, but I guess everybody else appreciated what we did.”

A Department of Agriculture rep told The Post, “Although the bakery has had repeated critical deficiencies that resulted in the revocation of its license, Caputo’s has the option to address those problems, reapply for a license, and, if granted, resume its business.

“Many businesses that have wanted to continue in operation have successfully pursued this course of action.”

Health inspectors noted during a Jan. 13 inspection that a live mouse was “present in the boiler room on open baskets of exposed breads which are human food by-products intended to be used as animal food.

“Floors/walls/ceilings throughout the establishment have surfaces that are observed to be in disrepair,” they also wrote.

Dusty shelves, a soiled walk-in cooler, broken equipment lid, over a hundred mouse droppings and a mouse carcass in the basement food storage area were observed, too.

Caputo argued the renovations needed to properly upgrade his business would have been too costly and cause it to shut down for months — at a time where it already “wasn’t easy to make a living,” he said.

“A lot of new places had come into the neighborhood, and I kind of kept my prices very low,” he said.

“The neighborhood wasn’t always as trendy as it is right now, and I kind of felt that I owed the customers who would shop with us for many, many years. I had to do right by them.”

Caputo told The Post he submitted a state-approved action plan — and even filled out the application to get his license back but then went “back and forth” over his decision to submit that, too.

“I’m being 100% honest, [the license revoking] was not the reason: I knew I had that under control and taken care of. I knew that we would’ve passed, but it was the right time” to leave, he said.

“I knew that if I didn’t do this now, I would never do it.”