Mr. Williams was long considered a leading candidate to replace Tim Cook as the company’s next chief executive.

Apple Inc. Chief Operating Officer Jeff Williams is retiring as the company’s longtime No. 2, marking a major changing of the guard at an already tumultuous time for the iPhone maker.

Having worked at Apple for nearly three decades, Williams has played a significant role in introducing the iPod and iPhone programs, leading the development of the Apple Watch, and overseeing the design team,