Mr. Mackey, in a conference call last month, acknowledged the impact the rising demand in organic foods was having on his company. “We’re doing all we can, but the reality is, there’s more competition,” he said. “Everybody is jumping kind of on the natural- and organic-food bandwagon, and that’s really, frankly, due to our success.”

Costco has become the biggest purveyor of organic foods, selling some $4 billion worth in the last year, compared with an estimated $3.6 billion in organic sales at Whole Foods, according to Kelly Bania, an investment analyst at BMO Capital Markets.

Walmart, which already had a robust organic business, announced last year that it was expanding the category, and General Mills and Campbell Soup have both announced intentions to expand the organic pieces of their businesses substantially.

To compete with stores offering goods at lower prices, Whole Foods has announced plans for a new store concept named for its private label line, 365, which will also sell some branded goods mainly aimed at millennial shoppers. The company has not said whether it plans to offer organic produce in the new stores, only that it will provide “high-quality, fresh foods.”

“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,” said Jeff Larkey of Route 1 Farms, who grows a variety of fruits and vegetables on 65 acres north of Santa Cruz, Calif. “Now they’re competing with the large supermarkets, and that may be one reason they’re trying to make conventional look better.”

Mr. Larkey used to sell to Whole Foods directly, but today, most of his products go to restaurants through distributors or to smaller grocers like New Leaf Community Markets. If Whole Foods gets any of his products, it does so through a broker in San Juan Bautista.