During his first term as president of the United States (2017–2021), Donald Trump and his administration repeatedly politicized science by pressuring or overriding health and science agencies to change their reporting and recommendations so as to conform to his policies and public comments. This was particularly true with regard to the COVID-19 pandemic, but also included suppressing research on climate change and weakening or eliminating environmental regulations.

Trump and his appointees pressured federal health and science agencies to take particular actions that Trump favored and to support his public pronouncements. He sometimes claimed that there was a "deep state" conspiracy among federal scientists, whose members delayed approval of COVID-19 vaccines and treatments because they wanted to hurt him politically or prevent his re-election.

Background Trump, inaugurated as president on January 20, 2017, did not name a Science Advisor to the President until July 2018, when he appointed meteorologist Kelvin Droegemeier to the position. Science advisory committees at multiple agencies including the Department of the Interior, the National Oceanic and Atmospheric Administration, and the Food and Drug Administration were disbanded. Many of Trump's first cabinet picks were people with a history of opposition to the agency they were named to head, including Rick Perry as Secretary of Energy and Betsy DeVos as Secretary of Education. In the science area the head of the Environmental Protection Agency (EPA), Scott Pruitt, had repeatedly sued the EPA when he was Oklahoma attorney general, and described himself as a "leading advocate against the EPA’s activist agenda".

Survey In a survey of scientists at 16 federal agencies conducted in 2018, 50% of respondents agreed that "the level of consideration of political interests hindered the ability of their agencies to make science-based decisions"; 69% of scientists at the U.S. Fish and Wildlife Service, 76% of respondents at the National Park Service, and 81% of scientists at the Environmental Protection Agency agreed.

Health agencies Suppressing and altering communications from health agencies On February 25, 2020, in the earliest days of the COVID-19 pandemic in the United States, a senior official with the Centers for Disease Control (CDC) said publicly that the spread of the virus in the U.S. was inevitable. This contradicted Trump's more optimistic predictions, and the CDC was largely banned from giving briefings on the coronavirus for the next six months.

In April 2020 political strategist and lobbyist Michael Caputo was appointed by the White House as assistant secretary for public affairs of the Department of Health and Human Services (HHS), in control of the department's communications strategy. Caputo appointed Paul Alexander, a Ph.D. health researcher, as his top advisor. They and other HHS officials attempted to control the content of information coming from the CDC whenever it was deemed to contradict or undermine what Trump was saying publicly.

In May 2020, according to documents released in April 2022 by the United States House Select Oversight Subcommittee on the Coronavirus Crisis, the Trump administration overruled the CDC's proposed guidelines for religious organizations. The CDC had warned that houses of worship were hot spots for coronavirus spread, but the White House removed from the guidelines all recommendations that churches consider online or drive-in services. Trump personally urged states to allow all houses of worship to reopen immediately and threatened to "override" any governors who did not do so.

In June 2020, the White House installed two political operatives with no public-health background at the CDC's Atlanta headquarters. Their responsibilities, according to CDC and administration officials, were to monitor CDC scientists and CDC Director Robert Redfield, as part of the ongoing effort to control the organization's public messaging. At first their role at CDC was undefined; one was later named Redfield's acting chief of staff and the other as her deputy. Although officially reporting to Redfield, they communicated regularly with Caputo and Alexander at HHS.

Caputo in June was trying to gain control of the Morbidity and Mortality Weekly Report (MMWR), a weekly publication issued by the CDC; it is the CDC's main vehicle for imparting current information and recommendations about public health to physicians, researchers, and the general public. In September 2020, it was reported that political appointees at HHS had tried repeatedly to change, delay, or remove reports about COVID-19 from MMWR if they undermined Trump's claims that the outbreak was under control. Caputo confirmed the September report, saying that his attempts to influence the content of MMWR had been going on for months. He said it was because the MMWR reporting contained "political content" as well as scientific information, adding that the changes suggested by his office were "infrequently" accepted by CDC. A MMWR report downplaying the benefit of hydroxychloroquine as a COVID-19 treatment was delayed for almost a month as Alexander questioned the political leanings of the authors. A report on the susceptibility of schoolchildren to the virus was also held up. Alexander demanded, unsuccessfully, that he be allowed to review and edit all issues of MMWR before they were published. On August 8, Alexander wrote to Redfield saying that "CDC to me appears to be writing hit pieces on the administration". He asked Redfield to change some reports that had already been published. Alexander later said that the CDC had written "pseudoscientific reports" and that he was in a better position to "make the judgment whether this is crap". CDC resisted many of the changes, but increasingly allowed HHS personnel to review articles and suggest changes before publication.

In August 2020, Emily J. Miller, a right-wing activist who had previously worked for the pro-Trump channel One America News Network and had no previous science or medical experience, was appointed as Assistant Commissioner for Media Affairs for the FDA, including being their top spokesperson, a role usually performed by non-political civil servants. Two weeks later, she was abruptly dismissed from the position, reportedly due to repeated clashes with the Agency's staff and a lack of aptitude for communicating in the medical and scientific field. Miller was subsequently appointed as the senior advisor to the chief of staff at the FDA. She described Regeneron's antibody cocktail, which was provided to Trump after he tested positive for COVID-19, as being "like a cure" for the disease.

In August and early September 2020, Alexander sent several messages to press officers at the NIH attempting to direct Anthony Fauci's media comments. Among his demands were that Fauci should refrain from promoting the wearing of masks by children in school and COVID-19 testing of children. Fauci later said that he had not received the messages and would not have been influenced by them if he had.

On September 16, CDC director Redfield told a Senate hearing that HHS and the White House Office of Management and Budget had ordered him to transfer $300 million from his agency's budget to HHS, to be spent on a public relations campaign directed by Caputo. He added that CDC had not been consulted about the proposed public relations campaign, which was intended to "bring America back". Caputo stated on Facebook that the program "was demanded of me by the president of the United States, personally." The goal was to get at least 20 celebrities to record messages to "restore hope" and "defeat despair" that would be broadcast before the November election. However, weeks before the election the program was reported to be "sputtering," because most of the targeted celebrities refused to participate and because the video firm hired to carry out the project, headed by a business partner of Caputo, had no prior experience with public health campaigns. On October 2, HHS Secretary Alex Azar told Congress that he had begun a review of the program to ensure that it would serve a public health purpose. On October 29, Politico reported that the program was no longer slated to run before the election and might not run at all. It was also reported that celebrities suggested for the announcements were vetted for their political opinions before being approached; if they had ever criticized Trump or expressed support for President Barack Obama, gay rights, or same-sex marriage they were ruled out. Reportedly 274 celebrities were considered but only 10 were approved.

In emails to Redfield, Alexander and Caputo repeatedly accused CDC scientists of attempting to "hurt the president" and writing "hit pieces on the administration". CDC employees described the period as a five-month-long campaign of bullying and intimidation. On June 30 Alexander strongly criticized an interview by Anne Schuchat, principal deputy director of the CDC, in which she described the extent of the pandemic and urged Americans to wear masks. Alexander accused her of lying and attempting to embarrass the president, and may have tried to get her fired. In another incident, Caputo repeatedly demanded to know who in the CDC press office had approved a series of interviews between a CDC epidemiologist and NPR, saying that he needed to manage department communications and "If you disobey my directions, you will be held accountable". He similarly threatened a CDC press official who had told CNN about an upcoming vaccine public relations campaign. On June 20, 2020, Alexander sent a message to CDC Director Redfield, criticizing a CDC report about risks to pregnant women from COVID-19. Alexander said that the report, whose limitations the CDC had acknowledged, would "frighten women" and give the impression that "the President and his administration can't fix this and it is getting worse". He said that in his "opinion and sense" the CDC was "undermining the president by what they put out".

On September 16, after the political influence over the CDC was reported, Caputo took a 60-day medical leave of absence and Alexander was fired. In an interview with the Toronto-based Globe and Mail after his departure from HHS, Alexander defended his actions, stating that he had wanted the CDC to make their reports "more upbeat so that people would feel more confident going out and spending money", and that he "did not think agencies should contradict any president's policy".

In September, Democrats on the House Oversight and Reform Select Committee on the Coronavirus Crisis launched an investigation into political interference with the CDC's reports and recommendations regarding the coronavirus. Charlotte Kent, the editor of MMWR, told the panel in December that she had been ordered to destroy an August 8 email from Alexander demanding that the CDC change a previously published report on coronavirus risks to children; she said that the email was deleted but she does not know by whom. Following her testimony, the Trump administration canceled previously scheduled interviews with four other CDC scientists and officials.

In December, the former CDC chief of staff, Kyle McGowan, and his deputy, Amanda Campbell, gave a series of interviews about their experiences. They described a years-long and escalating White House campaign to control and suppress the CDC during their tenure from 2018 until August 2020. They said the agency's science had been denied, its voice suppressed, and its budget siphoned off. McGowan said, "Everyone wants to describe the day that the light switch flipped and the C.D.C. was sidelined. It didn’t happen that way. It was more of like a hand grasping something, and it slowly closes, closes, closes, closes until you realize that, middle of the summer (of 2020), it has a complete grasp on everything at the C.D.C."