Investment analysts have speculated for years that Mr. Shaich, 63, has been looking for a way to reduce his role at the company after spending more than two decades building it up from a tiny 400-square foot cookie store in Boston.

Mr. Shaich, however, said that he planned to continue to lead Panera. “Nothing will change,” he said. “The management team and I will remain.”

With the acquisition of Panera, JAB will have spent more than $40 billion in what appears to be a big bet that it can muscle in on a market dominated by Starbucks and Nestlé.

Starbucks has just undergone a major management change, with its longtime chief executive, Howard Schultz, stepping aside to focus on developing its emerging high-end coffee business. Kevin Johnson, the new chief executive, served on the Starbucks board but made his career in technology.

In many ways, Mr. Schultz was the personification of the company, and under his leadership, Starbucks routinely posted record earnings and stellar growth, but it has run into some glitches recently. Investment analysts were spooked after the company reported first-quarter earnings in January that reflected slower sales in its vast fleet of American stores and problems with its mobile order system, which apparently could not keep up with demand.

One quarter does not, of course, a history make, and JAB also faces challenges.

It takes on Panera at a time when it has two large turnarounds on its hands, Krispy Kreme and Keurig Green Mountain. The doughnut chain was a phenomenon several years ago, then fell on hard times and has never fully recovered.

Keurig, which dominates the single-serve coffee market, has struggled as competition cut into its profitability. Then it made a big bet that fell flat on a single-serve machine to make cold drinks, and JAB stepped in.