FDA Commissioner Marty Makary to Resign After Clashing With Pharma, Trump, and His Own Agency

Food and Drug Administration Commissioner Marty Makary intends to resign Tuesday, according to two sources familiar with the matter, capping a turbulent 14-month tenure in which the surgeon-turned-regulator managed to anger pharmaceutical executives, vaping lobbyists, anti-abortion groups, and President Donald Trump himself — sometimes simultaneously.

The departure was already in the works before Makary was scheduled to testify on Capitol Hill Wednesday. It ends one of the most unconventional chapters in the FDA's modern history, one defined less by bureaucratic consensus than by a commissioner who seemed to treat the agency as a platform for challenging institutional orthodoxies across the political spectrum.

Makary arrived at the FDA in March 2025 with a reputation built during the COVID-19 pandemic as a critic of masks for children, vaccine mandates, and what he characterized as the CDC's overreliance on Israeli data in recommending boosters. Those positions made him a polarizing figure before he ever set foot in the commissioner's office, and they set the tone for what followed.

On vaccine policy, Makary moved aggressively. In May 2025, he appeared alongside Health and Human Services Secretary Robert F. Kennedy Jr. to announce the removal of the COVID-19 vaccine from the CDC's immunization schedule for "healthy children and pregnant women," arguing that "there's no evidence healthy kids need it today and most countries have stopped recommending it for children." The decision was celebrated by vaccine skeptics and condemned by pediatricians and public health officials who warned it would undermine confidence in the broader immunization schedule.

On food policy, Makary pushed what may become his most enduring legacy. He announced that the FDA and HHS would phase out eight artificial food dyes and colorings from the American food supply by the end of 2026, declaring that American children had been "living in a toxic soup of synthetic chemicals." He championed updated federal dietary guidelines that recommended limiting ultra-processed foods and refined carbohydrates while explicitly endorsing red meat and full-fat dairy — a direct reversal of decades of nutrition guidance.

"For decades, we've been fed a corrupt food pyramid that has had a myopic focus on demonizing natural healthy saturated fats, telling you not to eat eggs and steak and ignoring a giant blind spot: refined carbohydrates, refined sugars, ultra-processed foods," Makary said when announcing the new guidelines. "You don't need to tiptoe around fat and dairy. You don't need to push low-fat milk to kids."

The food dye initiative drew support from parents and health advocates across the political spectrum, but it also provoked fierce opposition from the food industry, which argued the timeline was unrealistic and the science behind synthetic dye bans was contested. Pharmaceutical companies, meanwhile, were already wary of Makary's willingness to challenge drug approval norms and pricing structures.

But it was Makary's stance on vaping that appears to have sealed his fate with the White House. In early May, Trump criticized Makary for not moving quickly enough to approve flavored vape and nicotine products, according to The Wall Street Journal. Trump's advisers informed him that Makary was delaying the president's effort to "save vaping," a pledge Trump made on social media during his campaign. A public health regulator refusing to fast-track nicotine products was politically intolerable for an administration that had promised the opposite.

Makary's resignation leaves the FDA without a permanent leader during a period of significant policy upheaval. The food dye phase-out will require sustained leadership to implement. The dietary guidelines he championed need enforcement. And the agency's vaccine policies remain a flashpoint that the next commissioner will inherit whether they want to or not.

What This Means For You: Makary's departure creates immediate uncertainty for two things that directly affect your daily life: what's in your food and what drugs reach the market. The artificial food dye phase-out is still scheduled for the end of 2026, but without Makary pushing it, the food industry will lobby hard to slow-walk implementation. The dietary guidelines endorsing full-fat dairy and red meat while warning against ultra-processed foods could also face revision under new leadership. And if you use vaping products, expect the approval pipeline for flavored nicotine to accelerate under a commissioner more aligned with the White House's priorities. The FDA doesn't stop running when a commissioner leaves, but the direction it runs in changes fast.