Last summer, a woman applied for an entry-level job at Sweet Stem Farm – what sounded like an idyllic homestead about eight miles north of Lancaster, Pennsylvania.

“Sweet Stem Farm is a small family farm in the heart of Pennsylvania Dutch Country,” according to the farm’s Web site. “With our high-touch approach to animal care, we produce some of the best-tasting, humanely-raised pork, beef and lamb in our region.”

The woman got the job. But Sweet Stem did not know that its new hire was an undercover agent of sorts: what the animal-rights activist group People for the Ethical Treatment of Animals (PETA) calls a “field observer.” Field observers help PETA, in its words, shine “a spotlight on the plight of animals who are abused on factory farms, in slaughterhouses, in laboratories, in circuses, and in other cruel industries.” And as they collect checks working in such industries, they are also being paid by PETA to stealthily document possible animal abuse.

And, during her two months at Sweet Stem Farm, PETA’s field observer – whom the organization has refused to name – uncovered quite the story. In graphic video, the woman filmed the reported abuse of pigs at the farm, surprising partly because of the operation’s connection to Whole Foods – a company, with disappointing earnings and stock trading near a 52-week low, that recently admitted to overcharging customers.

“If you’ve ever shopped at Whole Foods, you may have seen signs posted in the meat department that say things like ‘enriched environment’ and ‘treated humanely,'” the organization wrote in a press release. “But what a PETA investigator documented at a Pennsylvania pig farm that supplies Whole Foods reveals that these signs are probably worth less than the recycled paper they’re printed on.”

In a phone interview with The Washington Post, a PETA spokesman called the video “the first honest look at how these animals live before they are slaughtered for Whole Foods.”

“Whole Foods has . . . pushed this myth of so-called ‘humanely raised meat,'” Dan Paden, an associate director of evidence analysis at PETA, said. “People who do care, who are well-intentioned, are led to believe that they are buying meat from animals who lived happy lives. And these pigs did not live happy lives.”

He added: “In many ways, these animals lived and suffered just as they would on any factory farm.”

The video – which featured images of pigs, some allegedly sick and not given appropriate care, crowded into hot pens and roughly handled by employees – seemed to contradict Sweet Stem’s self-portrait.

“Our pigs are free-roaming in spacious straw-bedded greenhouse-style hoop barns,” the Web site of the farm, which PETA said supplies about 20 Whole Foods outlets in the Philadelphia area, read. “The kind of farming we do is described variously as local, sustainable, humane and eco-friendly. Whichever term you use, it’s a way of life for us.”

As explained in a video on the Whole Foods YouTube channel in 2009, Philip Horst-Landis first came to Sweet Stem, then named Meadow Run Farm, in 1999 after he answered a classified ad about pastureland for rent. The trip was the beginning of a love story: Horst-Landis ended up marrying the farmer’s daughter, Dee Horst-Landis, with whom he now co-owns Sweet Stem.

In 2007, the company started working with Whole Foods.

“We were starting out I think with, like, with four pigs a week,” he said. “So it wasn’t very much. We wanted to grow it to a little more than that. So were putting up new buildings to make that happen.”

Horst-Landis spoke of the challenges of raising animals humanely, but sounded committed to it.

“You need a specialty market for that,” he said. “I think all farmers probably deserve a better price, but especially ones that are really conscientious about the way they produce their food. . . . Because we really believe in the animal welfare part of it, we want to see every pig in the country raised this way.”

Sweet Stem is rated “Step 2″ on Whole Foods’ “5-Step Animal Welfare Rating Standards.” This system, developed by the Global Animal Partnership (GAP), “brings together farmers and ranchers, animal welfare advocacy organizations, scientists, and retailers” to improve the lives of animals, according to its Web site.

Step 2 means “no crates, no cages, no crowding.” Pigs are also supposed to be provided an “enriched environment” – “like a bale of straw for chickens to peck at, a bowling ball for pigs to shove around, or a sturdy object for cattle to rub against.” Farms rated “Step 5(plus)+,” the highest rating, have, among other amenities, free access to outdoor areas and ” live their entire lives on one farm.”

“Approximately 79 percent of all the pig farms that supply Whole Foods are Step 2 or lower,” Paden, PETA’s analyst, said. “. . . The vast majority of the farms in the Whole Foods system are this good or even worse, so to speak. In other words, it’s even more like a typical factory farm situation.”

In the wake of the PETA investigation, Whole Foods has removed the Sweet Stem video from its Web site.

“This blog post previously contained a video about Sweet Stem Farm dating back to 2009, before the implementation of GAP standards,” an editor’s note now reads. “We have taken the video down to prevent confusion. We market this product as GAP Step 2 in our stores, and the farm has been operating at a Step 2 rating since 2010.”

After an investigation, Whole Foods also stood by Sweet Stem.

“We made a visit to the farm within hours of being informed about the PETA video to evaluate farm conditions and practices with our own eyes and gather the facts,” Michael Silverman, a Whole Foods spokesman, wrote The Post in an e-mail. “We found that the farm conditions were in-line with GAP Step 2 certification. We did follow-up with the farm immediately regarding using the ear to restrain the pig so that a vaccine could be administered, and they agreed to stop that practice entirely.”

Horst-Landis, Sweet Stem’s co-owner, told Bloomberg the PETA video was “deceit and distortion.” But he also spoke of the perils of upscaling.

“When we were raising 80 pigs a year, raising pigs outside was feasible,” he said. “I didn’t understand that at a different scale that was difficult to pull off.”

Silverman of Whole Foods also offered a reminder about PETA’s philosophy. As the animal-rights organization said in its graphic Sweet Stem video: “There is no such thing as humane meat.”

“PETA’s agenda is very clear – a total end to animal agriculture,” Silverman wrote. “We respect and cater to a variety dietary choices represented across our diverse customer base, and our quality standards go well beyond what conventional grocers provide. No other grocer has done more than Whole Foods Market has to help move an entire industry toward higher levels of quality and improvements in animal welfare.”

Even after its overcharging scandal and as other supermarkets jump into the organic business it pioneered, Whole Foods enjoys a reputation as the place where those concerned about where their food comes from choose to shop. Indeed, the chain’s not-so-nice nickname – “Whole Paycheck” – indicates that some are willing to pay more for peace of mind.

But what if the peace of mind is illusory?

“Back in the day, Whole Foods was buying half of all the organic produce in the country – they helped a lot of organic farms get going,” Jeff Larkey, a California farmer, told the New York Times for a piece that questioned whether the market’s ratings systems are worthwhile. “Now they’re competing with the large supermarkets, and that may be one reason they’re trying to make conventional look better.”