Whole Foods Market (NASDAQ:WFMI) makes an interesting study in a floundering economy -- especially now that it's managed to increase its third-quarter profit. However, if CEO and founder John Mackey's provocative recent comments hold true, the upscale grocer's new strategic direction might take a serious bite out of its fortunes.

Appetizing signs
Third-quarter net income rose 26%, to $42.8 million, or $0.25 per share. This bested analysts' expectations for earnings of just $0.20 per share. In a heartening sign, revenue rose 2%, to $1.88 billion, although same-store sales dipped by 2.5%, versus a 2.6% increase last year. Still, comps did improve sequentially, so it looks like consumers are coming back.

It's nice to see not only a profit increase, but also a revenue increase, since Starbucks (NASDAQ:SBUX) and many other companies have been cutting costs amid falling sales. But those welcome numbers weren't Whole Foods' only bright spot. The company also raised its full-year earnings guidance -- a surprise for a high-end grocery, and a remarkable feat when rivals Wal-Mart Stores (NYSE:WMT), Costco (NASDAQ:COST), and SUPERVALU (NYSE:SVU) are struggling to increase their own profits.

In its conference call, Whole Foods said that some of competitors are emphasizing value and de-emphasizing organics. That seems to contradict recent evidence of the rise of private-label organics. But if competitors do start backing away from organic food, even as the public grows more aware of its benefits compared to conventional agriculture, Whole Foods could be poised to swoop in and capture more of the market.

Whole Foods generated $93 million in free cash flow in the quarter, and has $448 million in cash. If that piggy bank sounds impressive, don't forget the company also took on a hefty amount of debt when it purchased Wild Oats Market. Its long-term debt currently stands at $742 million.

Whole Foods vs. junk-food junkies?
CEO Mackey, no stranger to controversy, has now taken another provocative stance: criticizing his own company for selling "junk food." Say what?

Starting in the fall, the company will roll out a massive healthy-eating campaign -- exactly what Mackey described when he visited the Fool several weeks ago. Sure, the company benefited from the foodie gourmet trend, despite its decadence. But healthy eating resonates with Whole Foods' roots as a health-food store. Mackey reminded us that America's eating habits are following an ugly trend, and asked, "If Whole Foods doesn't educate people about how to eat healthier, who the heck is going to do it?"

Mackey went on record about the initiative in The Wall Street Journal, providing several "highly quotable" comments about the fatty indulgences on Whole Foods' shelves. The exec, himself a vegan, noted that healthy bulk foods now comprise about 1% of his company's sales.

His insistence led the Journal to speculate that Whole Foods may begin to back away from the processed and prepared foods it increasingly embraced as busy consumers shopped for convenience. I personally hope that won't happen until consumer demand compels it. Many consumers still like treats, and convenient meals -- healthful or otherwise -- fit their busy lifestyles.

I'm all for more education on healthier eating, and I believe that cooking is one of life's great pleasures. I also support Whole Foods' efforts to label genetically modified food, and its forward-looking championing of animal welfare. That said, I'd certainly miss prepared meals -- or the occasional brownie -- if they vanished from Whole Foods' shelves. A hoity-toity Whole Foods might drive customers away.

None of which contradicts the truth in Mackey's opinion: Many Americans could use more and better choices in their diet. (That sound you hear is McDonald's (NYSE:MCD) screaming in horror at the thought of losing its Big Mac-a-day regular customers.) If anything, Mackey may be ahead of the curve, since Congress is currently mulling a tax on fatty foods.

Indulge in moderation
Shares of Whole Foods, a longtime Motley Fool Stock Advisor pick, soared Wednesday following the announcement of its better-than-expected quarter. As a longtime shareholder, I'm not complaining that the shares hit a new high for the year. I'm also pleased to see increased revenue, however modest. I love the company's mission and philosophy, and I plan to hold shares for the duration, even if I occasionally snipe a bit.

But if you're thinking of chowing down on Whole Foods' shares, check their nutrition facts first. At 36 times earnings, the stock commands a rich, buttery premium compared to many of its rivals. (For example, Safeway (NYSE:SWY) trades at a mere nine times trailing earnings). While I still believe that Whole Foods has a bright future, conservative investors might want to wait for a lower-calorie price.

Further Mackey-tastic Foolishness:

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