There goes the neighborhood.

A Manhattan couple paid more than $1 million — a first — for an apartment in Brooklyn’s Bedford-Stuyvesant because the area reminds them of when the Lower East Side was gritty.

Young, hip people have been gentrifying Bed-Stuy for years because of cheap property prices — but a $1 million price tag for anything but an entire town house is unheard of.

“It reminds us of what the Lower East Side used to be like; that is why we bought there,” said new owner Mara Singer, who represents fashion and still-life photographers.

“We have been living on and off [on] the Lower East Side for 25 years. We do love it, but Soho House is coming, the neighborhood is changing and it is just different. We like the old Lower East Side.

“I guess it was a record-setting price, but it is still so much cheaper than Manhattan in so many ways,” she said.

Singer and her still-life photog husband, David Sawyer, snapped up the penthouse duplex on Lexington Avenue now that their two sons are moving to college this fall.

It’s a two-bedroom, two-bath loft condo that’s 1,559 square feet, with high ceilings and a 600-square-foot private roof deck.

The master bedroom is a loft, though, and the closest transit option is the unreliable G train.

“We live in a loft that is a little bigger,” Singer said. “What we are moving to is very, very similar to what we have now. We are loft people, but the new one is a more industrial, raw space. It’s not overdone, over-renovated and sanitized. It still has the old New York flavor, which doesn’t happen anymore.”

The new 32-unit, four-story condo building used to be a frozen-food factory, said broker Alex Maroni, of Douglas Elliman.

“It still has the magic,” Singer said. “They didn’t get rid of the beauty. They left a lot of it, which is what is so amazing.”

The condo really sold for $999,999 to avoid a special “mansion tax” added to homes that sell for more than $1 million, Maroni said.