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On Wednesday, Jana Partners said in a filing with the Securities and Exchange Commission that it was exiting its position of 26 million shares, or about an 8.2 percent stake in the grocery chain, making a profit of roughly $300 million.
Jana started selling its shares in Whole Foods on June 19, and then shed the remainder, 16 million shares, in a block trade at $41.66 apiece on Tuesday, the SEC filing shows.
Jana Partners in April first reported its ownership of Texas-based Whole Foods, bumping up shares of the supermarket company's stock. The hedge fund was, at the time, suggesting the struggling grocer should either accelerate its turnaround plans or consider putting itself up for sale.
In April, Jana said Whole Foods "shares are undervalued and represent an attractive investment opportunity." The investor group also pointed out it had "substantial experience" in the grocery and food sectors.
These purchases also made Jana Whole Foods' second-biggest shareholder.
The activist investor initially accumulated its stake in Whole Foods by buying stock priced between about $29 per share to about $32 per share, according to SEC filings. Considering where Whole Foods is trading today, Jana made a nice chunk of change, around $300 million, from its entire investment.
Jana's sales totaled more than $1 billion, and Jana originally paid about $794.5 million for its position in Whole Foods, the hedge fund disclosed.
A representative from Jana Partners didn't immediately respond to CNBC's request for comment.
Whole Foods' shares hardly moved Wednesday after the news broke. The grocery stock closed the day at $41.76 per share, hovering right around Amazon's $42 per share offer price.
In early June, prior to Amazon announcing its plans to acquire Whole Foods, Whole Foods' CEO John Mackey blatantly called out Jana Partners, tagging them "greedy bastards" who are only interested in making money from a forced sale of the struggling grocer.
"They're putting a bunch of propaganda out there, trying to destroy my reputation and the reputation of Whole Foods, because it's in their self-interest to do so," Mackey said in an interview with TexasMonthly.
Mackey's interview was published online days before the Amazon deal was announced.
Back when, Jana was frustrated that Whole Foods wasn't performing better in what was proving to be a competitive grocery market. Lately, more nontraditional players have swooped in and stolen market share; Lidl, a German grocer, just opened its first stores in the U.S. in June.
To be sure, Whole Foods' same-store sales have fallen for seven consecutive quarters. The company is scheduled to report earnings next Wednesday after market close.
Jana, meanwhile, has taken a similar tack in other investments it saw as underperforming. In 2013, the activist investor gained a 6 percent stake in Safeway, and then encouraged the grocer to exit certain markets and sell off non-core assets. In 2015, Jana acquired 7.2 percent of food packager ConAgra's shares and pushed them to divest weak assets after criticizing "persistent underperformance."
— CNBC's Sarah Whitten and Jeff Daniels contributed to this report.