John Mackey, the co-founder and chief executive of Whole Foods Market, refers to the company as his child—not just his creation but the thing on earth whose difficulties or downfall it pains him most to contemplate. He also sees himself as a “daddy” to his fifty-four thousand employees, who are known as “team members,” but they may occasionally consider him to be more like a crazy uncle. To the extent that a child inherits or adopts a parent’s traits, Whole Foods is an embodiment of many of Mackey’s. A Whole Foods store, in some respects, is like Mackey’s mind turned inside out. Certainly, the evolution of the corporation has often traced his own as a man; it has been an incarnation of his dreams and quirks, his contradictions and trespasses, and whatever he happened to be reading and eating, or not eating.

A year ago, Mackey came across a book called “The Engine 2 Diet,” by an Austin, Texas, firefighter and former professional triathlete named Rip Esselstyn. Basically, you eat plants: you are a rabbit with a skillet. Mackey had been a vegetarian for more than thirty years, and a vegan for five, but the Engine 2 book, among others, helped get him to give up vegetable oils, sugar, and pretty much anything processed. He lost fifteen pounds. This thinking about his body dovetailed with a recession that left many shoppers reluctant or unable to spend much money on the fancy or well-sourced food that had been the stores’ mainstay. Mackey, in a stroke of corporate transubstantiation, declared that Whole Foods would go on a diet, too. It would focus on stripped-down healthy eating. Fewer organic potato chips, more actual potatoes. He told the Wall Street Journal in August, “We sell a bunch of junk.”

The repudiation was rash, since Whole Foods would still be selling junk, of a kind. Mackey, an unrepentant foot-in-mouther, as often a fount of exasperation as of inspiration, tried to explain that his comment had been misunderstood. Mackey has been bewildered by the way some things that he has said or done have brought trouble on him and Whole Foods. Public opinion can be capricious and—when you’re a grocer, a retail brand, and a publicly traded company—hard to ignore or override.

Two years ago, Mackey passed through one of the roughest stretches of his life. The Bush Administration, in an uncharacteristic spasm of antitrust vigilance, was fighting Whole Foods’ purchase of a competitor, Wild Oats, contending that the merged company would unfairly corner what the Federal Trade Commission called the “premium natural and organic supermarket” sector. Meanwhile, the Securities and Exchange Commission was investigating Mackey: for nearly eight years, he had been secretly logging onto an Internet message board devoted to Whole Foods stock under the sock puppet, or pseudonym, “rahodeb” (an anagram of Deborah, his wife’s name), praising his own company, disparaging Wild Oats, and throwing in a flattering remark about his hair (“I think he looks cute!”). Mackey, for years a media and stock-market sweetheart, was suddenly recast as a monopolist, a fruitcake, and a sneak. The share price fell, and, even though the government eventually let the deal stand (with a few concessions from Whole Foods) and gave the sock puppetry a pass, many wondered how Mackey managed to hold on to his job.

During this period, Mackey sought succor in spiritual practice. He engaged a friend, a follower of the Czech transpersonal psychologist Stanislav Grof, to guide him through a therapeutic session of holotropic breathing. “I had this very powerful session, very powerful. It lasted about two hours,” Mackey said in an inspirational CD set he released last year called “Passion and Purpose: The Power of Conscious Capitalism.” “I was having a dialogue with what I would define as my deeper self, or my higher self.” He had a pair of epiphanies, one having to do with severed relationships that needed healing. The other was that “if I wanted to continue to do Whole Foods, there couldn’t be any part of my life that was secretive or hidden or that I’d be embarrassed [about] if people found out about it. I had to let go of all of that,” he said. “I’m this public figure now.”

He couldn’t “embarrass the company,” he told me. “I have to grow up”—he is fifty-six. “I can’t have affairs with women. One of the things that happened was you have more money and you have more opportunities for such things. And those are sort of off-limits. You can’t do that. Think of Mark Sanford, in South Carolina.”

His vows of discretion apparently allow for a great deal of latitude. He talks openly about his fixations and eccentricities—most of them, anyway. (“I am not going to talk about my sex life,” he told me, without my having asked him to.) His blend of guile and guilelessness is peculiar. “I no longer drink alcohol around journalists,” he said. He worries that he reveals too much. He can’t help but speak his mind, out of which spring confounding ideas and conventionally irreconcilable contradictions. The man who has perhaps done as much as anyone to bring the natural-foods movement from the crunchy fringe into the mainstream is also a vocal libertarian, an orthodox free-marketer, an admirer of Milton Friedman, Ronald Reagan, and Ayn Rand. In the 2008 Presidential election, he voted for Bob Barr—Ron Paul wasn’t on the ballot.

The right-wing hippie is a rare bird, and it’s fair to say that most of Whole Foods’ shoppers have trouble conceiving of it. They tend to be of a different stripe, politically and philosophically, and they were either oblivious or dimly aware of Mackey’s views, until the moment, this summer, when Mackey published an op-ed piece in the Wall Street Journal asserting that the government should not be in the business of providing health care. This was hardly a radical view, and yet in the gathering heat of the health-care debate the op-ed, virally distributed via the left-leaning blogs, raised a fury. In no time, liberals were organizing boycotts of Whole Foods. (Right-wingers staged retaliatory “buy-cotts.”) Mackey had thrown tinder on the long-smoldering suspicion, in some quarters, that he was a profiteer in do-gooder disguise, and that he, and therefore Whole Foods, was in some way insincere or even counterfeit. No one can say that he hasn’t brought it on himself.

“I have my own views, and they’re not necessarily the same as Whole Foods’,” Mackey told me. “People want me to suppress who I am. I guess that’s why so many politicians and C.E.O.s get to be sort of boring, because they end up suppressing any individuality to conform to some phony, inauthentic way of being. I’d rather be myself.”

“He’s a ready-aim-fire guy, and he’s not real disciplined in how he speaks his mind,” Gary Hirshberg, the C.E.O. of Stonyfield, the organic milk and yogurt producer, told me. “He has a really hard time reconciling his public and private selves.” Mackey’s resilience has surprised even those who, like Hirshberg, hold him in high esteem. “John has that Clintonesque ability to hang in there,” Hirshberg said. “He is Whole Foods management’s greatest asset but also, at times, its greatest challenge.”

Depending on where you are on the spectrum of epicurean cultural politics, you may consider Whole Foods to be a righteous grocer or a cynical con, a prod to self-improvement or a gateway to decadence, a neighborhood boon or a blight, a force for social good or a place to pick up chicks. To the likes of Wal-Mart and Costco, it has been an impetus to carry healthier, more judiciously sourced food. To small neighborhood natural- or gourmet-food shops, it has sometimes been an impetus to go out of business. It has enabled organic and artisanal producers to scale up, and put pressure on the giants to at least pretend that they are scaling down. It has less than a one-per-cent share of the American grocery market, yet it has unquestionably transformed the way Americans produce, buy, and eat food. Its name, justifiably or not, is shorthand for a food revolution.

To some, Whole Foods is Whole Paycheck, an overpriced luxury for yuppie gastronomes and fussy label-readers. Or it is Holy Foods, the commercial embodiment of environmental and nutritional pieties. To hard-core proponents of natural and organic food, and of food production that’s local, polycultural, and carbon-stingy, Whole Foods is a disappointment—a bundle of big-business compromises and half-steps, an example of something merely good that the perfect can reasonably be declared an enemy of. It’s a welter of paradoxes: a staunchly anti-union enterprise that embraces some progressive labor practices; a self-styled world-improver that must also deliver quarterly results to Wall Street; a big-box chain putting on small-town airs; an evangelist for healthy eating that sells sausages, ice cream, and beer.

The most perplexing paradox of them all, and in many respects their root source, is Mackey himself. I met him in a conference room at the company headquarters, in Austin. He slipped in through a door in the conference room and made a comment to a colleague about a book of Wendell Berry poems. We talked briefly about Frisbee golf, his game of choice. He was dressed in khakis, a pleather belt, trail shoes, and a green polo shirt with a Whole Foods logo. He is not a guy who cares a lot about how he looks, unless he cares a lot about appearing not to care. He has angular eyebrows and tousled hair. His disposition was serene, but you could sense a prickly, Jesuitical undercurrent coursing beneath it. He speaks softly, with a gentle Texas twang.

The health-care op-ed’s headline, “THE WHOLE FOODS ALTERNATIVE TO OBAMACARE,” was the Journal’s, Mackey says, but the sentiments were his. Mackey’s prescriptions ranged from the obvious (people need to eat better) to the market-minded (promote interstate competition among insurers) to the dreamy (the corporations will take care of us). The gist was that, together, they’d obviate the need for a federal plan, and that the course being pursued by the White House and the Democrats would have disastrous consequences. He led with an epigram attributed to Margaret Thatcher: “The problem with socialism is that eventually you run out of other people’s money.”

Before submitting the op-ed, he showed it to Lanny Davis, the former Clinton White House special counsel, who represented Whole Foods in its antitrust battle. Davis told me that he “prodded John a little to think like a liberal,” and he reckons that the Thatcher quote was ill-advised. Still, he blames “left-wing McCarthyism” for the outrage that greeted the piece.

“I was so viciously attacked for two reasons,” Mackey told me. “One is that people had an idea in their minds about the way Whole Foods was. So when I articulated a capitalistic interpretation of what needed to be done in health care, that was disappointing to some people.” He begrudges the extent to which people have projected onto Whole Foods an unrealistic and idealistic vision of the company. “The C.E.O. of Safeway, Steven Burd, wrote an op-ed piece in June advocating, basically, market solutions to the health-care problem, and nobody gave a shit,” he said.

Of course, Whole Foods has always held itself up as a paragon of virtue. It is an article of faith that it is, as Mackey often says, a mission-based business. It has seven “core values,” which are, broadly speaking, commitments to the fulfillment and equitable treatment of all “stakeholders”—customers, employees, investors, and suppliers—as well as to the health of the populace, of the food system, and of the earth. Whole Foods’ claim to righteousness is, in many respects, its unique selling point. If the mission is sincere, so is the commitment to making money. Mackey is adamant, and not merely unapologetic, that his company—any company—can and should pursue profits and a higher purpose simultaneously, and that in fact the pursuit of both enhances the pursuit of each. “Whole Foods itself is a market-based solution,” he said. “We’re a corporation. We are in capitalism. We have to compete with Safeway and Wal-Mart and Kroger and Wegmans and Trader Joe’s. What’s odd about it is that that’s what we’ve always been. We’re not a co-op.” To “the people that really dislike us,” he said, “Whole Foods is a big corporation, so they think that we’ve crossed over to the dark side. Kind of the Darth Vader myth, that somehow or another we’ve become bad because we’ve become large.”