• Deal allows outspoken Whole Foods co-founder to remain CEO
  • Activist investor Jana Partners has pushed grocer to seek deal

Amazon.com Inc. will acquire Whole Foods Market Inc. in a $13.7 billion deal, marking the biggest transaction ever for the e-commerce giant as it pushes deeper into groceries.

Amazon will pay $42 a share in cash for the organic-food chain, the companies said on Friday. John Mackey, Whole Foods’ outspoken co-founder and chief executive officer, will continue to run the business.

The deal sends a shockwave across both the online and brick-and-mortar industries, uniting two brands that weren’t seen as obvious partners. But Whole Foods came under pressure to find a buyer this year after activist investor Jana Partners LLC acquired a stake and began pushing for a deal. Jana’s move irked Mackey, who has referred to…