SEATTLE — Amazon.com Inc. will acquire Whole Foods Market Inc. for $13.7 billion, including debt, in the biggest deal ever for the e-tailer as it continues to encroach on the grocery sector. Amazon will pay $42 a share in cash for the natural food chain, the companies said this month. Whole Foods cofounder and chief executive officer John Mackey will continue to run the business.

“Millions of people love Whole Foods Market because they offer the best natural and organic foods, and they make it fun to eat healthy,” Jeff Bezos, Amazon’s founder and CEO, said in a statement. “Whole Foods Market has been satisfying, delighting and nourishing customers for nearly four decades — they’re doing an amazing job, and we want that to continue.”

“This partnership presents an opportunity to maximize value for Whole Foods Market’s shareholders, while at the same time extending our mission and bringing the highest quality, experience, convenience and innovation to our customers,” said Mackey.

Whole Foods will retain its name and Austin headquarters. Completion of the deal, expected to close by year-end, is subject to approval by the company’s shareholders and regulatory ­authorization.

Amazon’s biggest prior acquisition was three years ago, when it agreed to purchase video-game service Twitch Interactive Inc. for some $970 million in cash.

The Whole Foods purchase comes on the heels of Amazon’s opening to the public of two Seattle grocery pickup sites, which had been “beta tested” and accessible only to company employees before May. Amazon Prime members can now order groceries online and pick them up at the two drive-in facilities.

The brick-and-mortar openings are part of a push by Amazon for food sales that has included its decade-long offering of the AmazonFresh grocery delivery service. But the $14.99-a-month service hasn’t made a significant impact on the businesses of supermarketers and Walmart Supercenters. E-commerce accounted for 2% of grocery sales in 2016, according to Kantar Retail.

Amazon has also been operating a cashierless convenience store in Seattle, called Amazon Go. It was expected to open to the public early this year but has been available only to employees, reportedly because of problems with the technology.

C-store, fast food and online sales are all competing with traditional supermarketers for the $1.5 billion that Americans spend on food yearly, Kroger Co. CEO Rodney McMullen said this month. “We have to redefine the market as share of stomach,” McMullen remarked.

With Whole Foods having some 420 stores in 42 states, the acquisition is seen as a way to significantly boost Amazon’s brick-and-mortar offering of consumables. But Whole Foods has been having its own problems with market share — with same-store sales dropping for nearly two years — and major shareholders pressing for the company to consider a sale.

The chain in May restructured it leadership, replacing five directors, naming a new board chair and making official the hiring of a new chief financial officer. The overhaul was described as part of the company’s “accelerated path to delivering shareholder value.”

Mackey at the time outlined several initiatives aimed at helping the company he cofounded in 1978 meet newly stated financial goals for 2020. They included the rollout of a customer loyalty program being tested in Philadelphia and Dallas to all U.S. stores by the end of the year; increased reliance on data analytics to guide purchasing decision, with a goal of “lower costs, lower prices and higher sales;” and $300 million in cost savings by the end of 2020.

But Jana Partners, the hedge fund that holds a nearly 9% stake in Whole Foods and went public with its criticism of the company’s direction in April, asserted that the new board members lacked the grocery industry experience needed to oversee a turnaround. Jana had also called on the chain to consider putting itself up for sale, an option endorsed by mutual fund manager Neuberger Berman, which owns just under 3% of the ­company.

The management shake-up came as Whole Foods reported a 2.8% decline in same-store sales in the second quarter and a 3% drop in the number of transactions in the period.