Following the inauguration of President Trump in January, the U.S. experienced a whirlwind of changes at federal food safety and public health regulatory agencies throughout 2025. The volume of activity and the breakneck speed at which firings and hirings, restructurings, policy changes, program and budget cuts, and other actions occurred—and in some cases, were reversed—made it difficult for food safety professionals, industry, media, and the public alike to keep track of or understand what was happening inside of critical government offices.

To make it a bit easier to grasp the scope of how the second Trump Administration has affected federal agencies relevant to food safety, this article summarizes Food Safety Magazine’s coverage throughout the year on the major happenings at the U.S. Department of Health and Human Services (HHS), the U.S Food and Drug Administration (FDA), the U.S. Centers for Disease Control and Prevention (CDC), and the U.S. Department of Agriculture (USDA).

Below is a comprehensive timeline of U.S. federal food safety changes under the Trump Administration in 2025, with a brief explanation of each event and links to the original news stories.

A 2025 Timeline: Changes at Federal Food Safety and Public Health Regulatory Agencies Under the Trump Administration

Top story—January 23: FDA, CDC Ordered to Temporarily Pause All External Communications, Obtain Trump Admin Approval. On January 21, the day after President Trump’s inauguration, HHS directed federal public health agencies—including FDA and CDC—to halt all external communications until February 1, pending review by presidential appointees. The freeze covered regulations, guidance, press releases, social media, and even public speaking engagements, with exceptions only for legally required or critical health and safety updates. While FDA began issuing limited outbreak advisories in early February, CDC remained largely silent until late in the month.

Top story—January 28: USDA Inspector General Phyllis Fong Dismissed by Trump Administration. The Trump Administration dismissed 17 Inspectors General across federal agencies, including Phyllis K. Fong, who had served as USDA’s Inspector General since 2002. Fong oversaw audits, investigations, and enforcement efforts aimed at ensuring efficiency and preventing fraud within USDA programs. Notably, Ms. Fong had recently ordered an internal probe after the 2024 listeriosis outbreak linked to Boar’s Head deli meats, which exposed gaps in USDA’s inspectoral oversight of regulated facilities. Other removed officials at agencies with some relevance to food safety included Christi Grimm of HHS and Sean O’Donnell of the U.S. Environmental Protection Agency (EPA).

February 17: Brooke Rollins Confirmed as Secretary of Agriculture, Cites 'Aggressive Plan' to Eliminate USDA Jobs. On February 13, Brooke Rollins was confirmed as the 33^rd U.S. Secretary of Agriculture in a 72–28 Senate vote. A longtime Trump policy advisor and former head of the America First Policy Institute, Rollins signaled sweeping workforce changes at USDA, including eliminating positions deemed “unnecessary.” Within days, probationary employees at USDA’s National Institute of Food and Agriculture (NIFA), Agricultural Research Service (ARS), and Economic Research Service (ERS) were dismissed. The cuts reportedly disrupted avian influenza response efforts, prompting USDA to seek to re-hire these fired employees—but the agency struggled to recover its lost bird flu response staff.

February 17: RFK Jr. Confirmed as HHS Secretary; Widespread Firings Coming to FDA, CDC. On February 13, Robert F. Kennedy Jr. (RFK Jr.) was confirmed as the U.S. Secretary of Health in a 52–48 Senate vote, bringing his "Make America Healthy Again" (MAHA) agenda to the White House. Shortly after confirmation, he signed an executive order creating the MAHA Commission, which was tasked with assessing health risks from food ingredients and chemicals and developing a federal strategy to combat childhood chronic disease. The commission includes leaders from HHS, USDA, FDA, CDC, and EPA. Meanwhile, sweeping HHS workforce reductions loomed, with about 5,200 positions being cut across public health agencies including FDA and CDC—where nearly half of the latest class of “disease detectives” were eliminated. USDA has also dismissed probationary employees as part of similar restructuring efforts.

Top story—February 18: FDA Leader Jim Jones Resigns After 89 ‘Indiscriminate’ Firings in Human Foods Program. Jim Jones, FDA’s first Deputy Commissioner for Human Foods, resigned on February 17, 2025, citing 89 “indiscriminate” layoffs in the Human Foods Program that he said made it “fruitless” to continue his work. Jones, who led FDA’s ban on red dye 3 and aimed to strengthen food chemical oversight, warned that cuts included staff with critical expertise in nutrition, infant formula, and food safety response. Reportedly, one of the FDA staffers whom the Trump Administration fired—and then scrambled to re-hire—was a top official in charge of infant formula safety.

February 19: Major Advocacy Groups Say Mass Layoffs at FDA Could Jeopardize Food Safety, ‘MAHA’ Agenda. A coalition of important public health, food industry, and consumer advocacy groups raised alarms over the firing of FDA Human Foods Program staff and the resignation of Deputy Commissioner Jones, marking the first of many instances in which stakeholders would voice similar concerns. The groups warned that under-resourcing FDA would undermine food safety, outbreak response, and efforts to tighten control on chemical additives—stated priorities of Secretary Kennedy’s MAHA agenda.

February 21: Attorney Kyle Diamantas Expected to Replace Jim Jones as FDA Deputy Commissioner of Human Foods. Without public fanfare, Kyle Diamantas, J.D., replaced Jim Jones as Deputy Commissioner for Human Foods. Diamantas, formerly a partner at Jones Day, is experienced in regulatory, compliance, and enforcement matters involving FDA-regulated goods. Of note, he previously defended Abbott Laboratories in a lawsuit accusing the company of failing to adequately warn parents that its specialized formula for premature infants was associated with an elevated risk of a deadly bowel condition.

February 25: FDA Moves to Rehire Some Human Foods Staffers Who Were Previously Fired. After the reality of mass layoffs began to set in, FDA reportedly asked some terminated employees to return, including at least ten staffers responsible for reviewing food ingredient safety. Sources said the agency aimed to rehire about 300 employees across drug, food, medical device, and tobacco programs. The cuts disproportionately affected probationary employees in critical areas, including FDA’s newly established Human Foods Program. While some food safety positions were reinstated, rehiring efforts appeared to be driven largely by pressure from the medical device industry and were therefore focused in that area.

February 26: Letter From 85 Congresspeople Urges End to Federal Public Health ‘Gag Order,’ Addressing Bird Flu. Amid the communications freeze, 85 members of Congress sent a letter to President Trump criticizing the “gag order,” warning it was hampering efforts to control the ongoing HPAI H5N1 outbreak affecting dairy cattle and poultry flocks. Lawmakers urged the administration to restore cross-agency collaboration, resume timely public health communications, and support surveillance programs like the National Milk Testing Strategy. The letter also condemned recent layoffs of USDA employees working on bird flu response, calling the actions contradictory to stated priorities.

March 5: U.S. Office of Personnel Management Walks Back Orders to Fire Federal Employees After Court Ruling. A federal judge issued a temporary restraining order against the U.S. Office of Personnel Management (OPM), stating that the agency lacked authority to mandate the sweeping termination of probationary federal employees. On March 4, OPM clarified that agencies retained full authority over personnel decisions and were not required to take performance-based actions.

Top story—March 7: Key Federal Food Safety Advisory Committees, NACMCF and NACMPI, Have Been Terminated. USDA terminated two longstanding food safety advisory committees: the National Advisory Committee on Microbiological Criteria for Foods (NACMCF) and the National Advisory Committee on Meat and Poultry Inspection (NACMPI). These panels provided impartial scientific guidance to USDA, FDA, and CDC on critical food safety issues, including Listeria control, Cronobacter in infant formula, and inspection standards. The decision was widely criticized by food safety experts, public health stakeholders, and legislators.

March 7: FDA Spending Freeze Leaves Staffers Feeling ‘Dangerously Unprepared’ for Next Foodborne Illness Outbreak. An investigation by Consumer Reports was published, in which FDA Human Foods Program staff reported that a spending freeze imposed on January 23 left them unable to perform routine tasks such as purchasing food samples for testing, acquiring lab equipment, or maintaining subscriptions to scientific journals. Staffers said that emergency purchase requests required a confusing, multi-step approval process that could take up to two weeks, creating delays that jeopardized outbreak investigations and food safety oversight. Employees warned that reduced testing and resource shortages could allow contaminated products to remain on shelves, leaving the agency “dangerously unprepared” for the next foodborne illness emergency.

Top Story—March 20: FDA Delays FSMA 204 Traceability Rule Compliance Date by 30 Months. FDA extended the compliance date for its long-awaited Food Traceability Final Rule, which fulfils Section 204(d) of the Food Safety Modernization Act (FSMA 204), pushing compliance from January 20, 2026 to July 2028. FDA stated that the rule’s requirements remain unchanged and emphasized that full compliance across all regulated entities is necessary to achieve the rule's intended public health benefits.

March 26: Dr. Marty Makary Confirmed as FDA Commissioner, Says He Will Review Recent Mass Layoffs at Agency. Marty Makary, M.D., M.P.H., was confirmed as FDA Commissioner on March 25 in a 53–47 Senate vote, and was sworn in on April 1. A surgeon and public health researcher, Makary previously criticized FDA leadership and pledged during his confirmation hearing to align the agency with the administration’s MAHA agenda, emphasizing food’s role in health. He also said he would review the mass layoffs at FDA that occurred just prior to his appointment—a commitment that was never publicly revisited.

March 27: Thousands More Layoffs Coming to FDA, CDC as HHS Announces Major Restructuring. HHS announced a major restructuring under its “Transformation to Make America Healthy Again” initiative, cutting about 10,000 positions department-wide, including 3,500 at FDA and 2,400 at CDC. Consumer advocates warned the cuts could undermine food safety oversight, despite HHS assurances that front-line scientists and inspectors would not be affected.

Top story—April 7: As U.S. Pieces Together How HHS Cuts are Affecting Food Safety, Stakeholders Speak Out. Following the implementation of the thousands of layoffs announced by HHS on March 27, a picture of what these cuts mean for food safety came into focus. Despite assurances that front-line scientists and inspectors would be spared, reports indicated cuts to veterinarians, toxicologists, microbiologists, and entire units such as CDC’s Lead Poisoning Prevention Branch and FDA’s Division of Food Processing Science and Technology. Stakeholders warned that FDA’s food safety capacity was disproportionately weakened, and that the reductions threatened initiatives like Operation Stork Speed, which aims to improve infant formula safety. Congressional leaders called on Secretary Kennedy to explain the impact of the cuts, and critics argued that the layoffs undermine the administration’s stated MAHA objectives. State food inspection programs, which conduct most FDA inspections, also faced steep funding cuts, compounding concerns about foodborne illness prevention and contamination control.

April 8: HHS' Proposed FDA Reorganization Would Drastically Alter Structure of Agency, Eliminate Product-Specific Offices. A leaked plan suggested the possibility of FDA undergoing another major restructuring, just months after the official launch of the new Human Foods Program in October 2024. The proposal reportedly sought to eliminate product-specific offices and consolidate all review divisions—covering drugs, biologics, devices, tobacco, and foods—into a single regulatory office, alongside new offices for inspections, policy, shared services, and innovation. Critics warned that such changes would dismantle specialized centers, reverse years of progress, and increase political interference, thereby undermining food safety and other regulatory priorities. It is worth noting that these rumored proposals have not come to light in any official capacity.

April 18: Rumored FDA Budget Proposal Would Cut Funding, Move Routine Food Inspections to States. It was revealed that FDA had suspended its quality control program for food testing labs and halted efforts to improve avian influenza testing in dairy and pet foods due to recent staff reductions. At the same time, draft White House budget documents suggested that FDA was facing a 17 percent funding cut in Fiscal Year (FY) 2026, reducing its budget to $6.5 billion and shifting all routine food facility inspections to states. The leaked draft budget information has not yet been confirmed, and the exact details of FDA's FY 2026 budget are unclear.

Top story—April 24: USDA Withdraws Proposed Regulatory Framework for Salmonella in Poultry After Years of Development. USDA’s Food Safety and Inspection Service (USDA-FSIS) withdrew its proposed regulatory framework for Salmonella in raw poultry. The agency cited the need for further consideration of public comments, despite years of development and stakeholder input, including guidance from the now-disbanded NACMCF.

April 29: FDA Reportedly Reinstating Some Fired Food Safety Scientists, Inspection Support Staff. FDA began reinstating some food safety scientists and laboratory staff, as well as several dozen inspectoral support employees, after erroneous layoffs disrupted critical programs. The terminations, blamed by HHS on inaccurate Human Resources data, suspended food safety sting programs, stalled foreign inspections, and delayed repayment of business expenses incurred by inspectors.

May 2: White House FY 2026 Budget Request Includes Sparse Details on 'MAHA' Food Safety. The Trump Administration sent its FY 2026 discretionary budget request to Congress, proposing a 23 percent cut in non-defense spending—the lowest level since 2017. The request included funding to expand efforts under Secretary Kennedy’s MAHA agenda, such as creating MAHA food boxes to replace the Commodity Supplemental Food Program, but provided few details on allocations for food safety work.

May 5: More Than 15,000 USDA Employees Take Trump Administration's Resignation Offer. More than 11,300 U.S. Department of Agriculture employees signed up for the Trump Administration’s second round of deferred resignations, following nearly 3,900 departures earlier in the year, bringing total staff resignations to over 15 percent of the agency’s workforce. The resignations include hundreds of food safety inspectors and technical experts.

June 12: HHS Budget Request Beats Familiar Drum. HHS proposed a $94.7-billion budget for FY 2026, including $6.8 billion for FDA—a $271 million decrease from FY 2025—with $1.2 billion allocated to the Human Foods Program. The request earmarked $234.6 million for MAHA priorities, such as improving nutrition, controlling food additives, and addressing food safety, alongside $14.7 million for modernizing infant formula oversight. Additional funding included $97.8 million to strengthen food safety, $33 million to expand state partnerships for routine inspections, and $6.8 million to support critical laboratory operations.

July 31: Senate Confirms Dr. Susan Monarez as CDC Director. On July 29, Senate confirmed Trump nominee Susan Monarez, Ph.D. as CDC Director in a 51–47 vote, making her the first non-physician to lead the agency in over 70 years and the first CDC Director to require Senate confirmation under a 2023 law.

Top story—August 26: CDC Slashes FoodNet Surveillance From Eight Foodborne Pathogens to Two. CDC quietly scaled back its FoodNet surveillance program on July 1, with the cuts only coming to light in August. Citing inadequate funding, the agency slashed FoodNet coverage from eight important foodborne pathogens to only Salmonella and Shiga toxin-producing Escherichia coli (STEC). Experts warned the cuts could hinder outbreak detection and trend analysis, as pathogens like Campylobacter and Listeria monocytogenes are no longer actively monitored. While CDC noted that other passive surveillance systems remain in place, food safety experts stressed that FoodNet was the only active, multi-pathogen federal surveillance system.

Top story—August 28: Trump-Appointed CDC Director Dr. Susan Monarez Fired After Clashes With Secretary Kennedy. Recently confirmed CDC Director Dr. Monarez was removed from her role by the White House following a public dispute on social media platform X. The Trump Administration attributed her dismissal to misalignment with MAHA, while her attorneys said she was fired due to her refusal to “rubber-stamp unscientific, reckless directives and fire dedicated health experts” at the behest of Secretary Kennedy. Top CDC officials and veteran staffers—whom Dr. Monarez was reportedly asked to fire—resigned in protest after Dr. Monarez was dismissed. Among those who resigned was Dan Jernigan, M.D., Director of the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), which is responsible for tracking foodborne illness outbreaks, zoonotic diseases, and antimicrobial resistance.

August 29: RFK Jr.’s Second in Command Named CDC Acting Director Following Sudden Firing. Jim O’Neill, former Deputy Secretary of HHS, who does not have training in medicine or infectious disease science, was appointed CDC’s Acting Director in place of Dr. Monarez.

September 4: Public Health Professionals, Groups Demand Resignation of HHS Secretary RFK Jr. In two letters signed by thousands of individuals and dozens of groups, public health and food safety professionals called for Secretary Kennedy to resign, accusing him of undermining science, weakening food safety protections, and endangering public health.

September 9: What the Final MAHA Report Could Mean for Food Safety. The MAHA Commission's final strategy report was published in September, a month after it was expected to be released. It received criticism for its deregulatory stance and lack of detail, leaning heavily on voluntary industry action rather than enforceable rulemaking. Stated goals in the report include phasing out synthetic food dyes, closing the Generally Recognized as Safe (GRAS) self-determination pathway for food ingredients, updating water quality standards, and reforming infant formula oversight—though experts noted that most initiatives lack clear timelines or regulatory teeth. Stakeholders expressed skepticism about the administration’s ability to deliver meaningful change, citing budget constraints and vague language in the report. Critics also flagged the report’s pesticide section for echoing industry talking points and omitting stronger protections against chemicals linked to health risks.

October 1: Government Shutdown Affects Food Safety: HHS Furloughs Employees, FDA Pauses CORE Investigation Table. Due to the federal government shutdown that began on October 1, FDA initially announced it would pause weekly updates to its Coordinated Outbreak Response and Evaluation (CORE) Investigation Table, which tracks foodborne illness outbreaks, while continuing emergency response and surveillance activities. The agency walked that statement back on October 3, clarifying that CORE updates would proceed as usual, alongside public health advisories when actionable information emerges. The shutdown, which lasted through November 12, affected 41 percent of HHS staff and prompted concerns about delays in long-term food safety initiatives.

October 10: Federal Layoffs to Hit HHS Amid Government Shutdown, May Affect Food Safety Staffers. The Trump Administration announced plans for mass layoffs of furloughed federal employees due to the government shutdown, with HHS among the first agencies targeted.

October 14: Entire Departments of CDC Outbreak Experts Fired, Rehired During Shutdown RIFs. The Trump Administration fired approximately 1,300 CDC employees during the shutdown but reinstated roughly 700, leaving around 600 permanently laid off. The layoffs briefly threatened those in valuable public health roles, including the entire Morbidity and Mortality Weekly Report (MMWR) editorial team and 70 outbreak investigators.

Top story—November 6: Analysis Shows FDA Foreign Facility Inspections Hit Historic Low After Trump Admin Cuts. Foreign food safety inspections by FDA fell to new lows in 2025 after Trump Administration budget cuts and mass layoffs reduced agency resources. ProPublica reported that monthly foreign inspection numbers fell by nearly half in March and remained about 30 percent lower through July compared to previous years, despite FDA’s stated goal to expand unannounced foreign inspections.

November 13: Shutdown Deal Restricts Funds for FSMA 204, Produce Safety Rule Enforcement. The FY 2026 appropriations bill that ended the historic government shutdown allocated $1.17 billion to FDA’s Human Foods Program and related activities, while imposing limits on enforcement of the FSMA Food Traceability Final Rule and the FSMA Final Rule on Produce Safety. It also restricted FDA from issuing new Listeria monocytogenes guidelines for low-risk ready-to-eat foods and directed the agency to begin evaluating pet food labeling and ingredient regulation. Additionally, the bill mandates quarterly engagement with industry on FSMA 204 flexibilities and requires FDA to provide recommendations ahead of full compliance.

November 17: Federal Workforce Data Reveal Impact of Trump Admin RIFs on USDA Food Safety Expertise. An analysis of U.S. Office of Personnel Management (OPM) data by the National Sustainable Agriculture Coalition showed that Trump-era workforce cuts severely impacted USDA-FSIS and USDA's Animal and Plant Health Inspection Service (USDA-APHIS), which lost 8 percent and 20 percent of staff, respectively, between January and March 2025. More than 15,000 USDA employees have accepted voluntary resignation offers, including hundreds of food safety inspectors and technical experts, and upcoming reorganization plans could trigger further losses as staff face relocation and consolidation of critical functions.

December 19: Dr. Mindy Brashears Confirmed as Head of USDA-FSIS. Career food scientist and microbiologist Mindy Brashears, Ph.D. was confirmed by the Senate in a 53–42 vote for a second term as Under Secretary of Agriculture for Food Safety, a role in which she will oversee USDA-FSIS. She previously served in the same position from 2020–2021 during President Trump’s first term. In Senate confirmation hearings, Dr. Brashears stated that her top priority as Under Secretary for Food Safety would be Salmonella control. Food industry associations applauded her confirmation and her track record for science-based decision-making.