Amazon's biggest bet yet will test Jeff Bezos' ability to absorb another company into the e-commerce giant.
Amazon's $13.7 billion tie-up with Whole Foods is 14 times larger than Amazon's 2014 deal to buy video game streaming platform Twitch for $970 million, including debt. Its scale presents challenges to Amazon in a way prior deals -- for companies that tended to be managed independently -- have not.
"This is a much more transformational acquisition," Ben Schachter, an internet analyst at Macquarie, told CNBC in a phone interview. It "may add a fourth pillar to the Amazon ecosystem."
Analysts say Whole Foods solves Amazon's problem of trying to develop grocery delivery through its Amazon Fresh business, which has struggled to grow over the last decade even as Bezos made Prime a key part of the Amazon empire.
Whole Foods' network of food stores solves a disconnect that had existed between Prime customers and the nascent food business, analysts said.
"I think the most important aspect of the purchase is that it gives Amazon 440 refrigerated distribution centers in the U.S. and probably puts their distribution presence within 10 miles of 80% of the population and within 90% of the wealthy population," Michael Pachter, managing director, equity research, at Wedbush Securities, said in an email to CNBC.
"Amazon Fresh has had little traction because consumers don't have confidence that the perishable products they purchase will be of high quality," he said. "The acquisition of WFM removes this concern, as Whole Foods' brand image is outstanding."
Schachter said he expects the Whole Foods integration into Amazon to be more "hands-on" than Amazon's prior deals. "Whenever I see a deal like this I think how does it impact the Prime ecosystem?" he said. "This one is quite different in terms of its scale and impact on importance."
Some of Amazon's earlier deals haven't turned out well. Twitch has grown since the acquisition, but two other large purchases, for Zappos and Quidsi, have faced challenges.
Amazon bought online shoe retailer Zappos for $930.1 million in July 2009 and let the firm's management, including entrepreneur Tony Hsieh, run it, including the decision to shift to a distinctive workplace culture that eliminated hierarchy. However, when the switch happened in April 2016, 18 percent of Zappos employees took a buyout offer and left, according to The Washington Post.
Zappos' attempt to move to Amazon's cloud computing system froze the company's website and took months longer than expected to complete. As a result, more than a third of 130 Zappos engineers left, according to The New York Times.
Zappos did not return a CNBC request for comment.
Amazon bought Quidsi, operator of e-commerce sites like Diapers.com and Soap.com, about seven years ago for $545 million but said in March it was shutting it down after it failed to reach profitability. The closure will result in more than 260 layoffs, according to a New Jersey state filing.
In the fourth quarter of 2015, Amazon began redirecting inventory from Quidsi's three fulfillment centers to Amazon's own warehouse network, sources told CNBC.
Amazon's own tough, cost-conscious work culture was the subject of a 2015 New York Times story. In contrast, Whole Foods has made Fortune magazine's "100 Best Companies to Work For" list every year since 1998, according to Whole Foods' website.
However, Whole Foods has struggled as business. The company reported a seventh-straight quarter of negative same-store sales in its fiscal second quarter.
"Whole Foods needs to make changes to respond to their own company's environment. In that way I think Amazon has its own plans for how to position the company," said Joseph Agnese, an analyst at CFRA Research.
Agnese said without the need to report as a public company, Whole Foods could also undercut competitors and sell groceries at a loss.
A Whole Food spokesperson wouldn't comment. Amazon did not immediately respond to a CNBC request for comment.
As for worries about technology immediately taking away jobs at Whole Foods, Amazon doesn't plan now to automate cashier jobs at Whole Foods or lay off employees as a result of the deal, Drew Herdener, spokesman for Amazon, told The New York Times.
"I doubt we'll see any change to the culture at WFM," Wedbush's Pachter said. "They will continue to manage retail, and their sales should expand dramatically as they add online ordering and delivery capability. Profitability should increase dramatically as well."
Whole Foods may mark the beginning of more big acquisitions for Amazon. The e-commerce giant is interested in acquiring Slack, an internal messaging platform for companies, for at least $9 billion, Bloomberg reported this week, citing sources. Amazon did not immediately return a CNBC request for comment.
Watch: Is a Whole Foods bidding war coming
