Food and Drug Administration Commissioner Marty Makary is stepping down after a turbulent 13-month term marked by organizational upheaval, controversies over drug approvals and tensions with the White House.Kyle Diamantas, the agency's deputy commissioner for food, will serve as acting commissioner, according to sources familiar.Why it matters: Under Makary, FDA became the unexpected source of drama and a lightning rod for Health Secretary Robert F. Kennedy Jr.'s broader efforts to upend health policy.His departure means the Trump administration will be seeking to fill three Senate-confirmed health positions, including vacancies for Centers for Disease Control director and surgeon general. Driving the news: Makary, a Johns Hopkins physician and researcher, faced a series of controversies over abortion pills, flavored vapes, vaccines and rare disease drugs as the agency he oversaw underwent substantial turnover.He faced internal criticism for not accommodating some of President Trump's priorities, along with complaints from health care investors about unpredictable regulatory decisions that rejected some promising drugs.Makary launched initiatives to streamline some of the FDA's regulatory functions — including real-time clinical trials and the awarding of vouchers to speed up reviews of some treatments deemed in step with the administration's priorities. He also took steps to reduce animal testing. But Makary remained a magnet for controversy. For example, President Trump had to pressure him to approve flavored vapes after Makary initially resisted, The Wall Street Journal reported. Anti-abortion groups called for Makary to be fired, frustrated that he didn't roll back liberalized rules for obtaining the widely used abortion pill mifepristone and reinstate in-person dispensing requirements. Indeed, under his tenure the FDA approved a generic version.Under Makary's leadership, the FDA also drew controversy for rejecting certain rare disease drugs. Biologics division chief Vinay Prasad, who has also since left the agency, was at the center of those decisions as well.Asked on Tuesday if he fired Makary or asked him to resign, Trump replied, "Well, I don't want to say, but Marty is a great guy. ... He was having some difficulty.""Marty's a terrific guy, but he's going to go on and he's going to lead a good life," Trump said.The big picture: Makary came into the role as a respected Johns Hopkins physician, but quickly faced turmoil. His confirmation came as DOGE laid off many health agency staff and the agency grappled with turnover in key roles. The FDA's drug center cycled through a string of four different directors in a year. What's next: As the administration looks to pivot away from vaccine controversies, President Trump's choice to replace Makary will send a strong signal about whether he's really looking for policy changes."Finding someone industry welcomes and MAHA does not despise may be a bit of a challenging channel to navigate," Raymond James analyst Chris Meekins wrote in an investor note prior to the announcement.