WASHINGTON—The Biden appointee in charge of the nation’s most treasured documents has over the past year ignited a behind-the-scenes fight over the telling of American history.

U.S. Archivist Colleen Shogan and her top advisers at the National Archives and Records Administration, which operates a popular museum on the National Mall, have sought to de-emphasize negative parts of U.S. history. She has ordered the removal of prominent references to such landmark events as the government’s displacement of indigenous tribes and the incarceration of Japanese-Americans during World War II from planned exhibits.

Visitors shouldn’t feel confronted, a senior official told employees, they should feel welcomed. Shogan and her senior advisers also have raised concerns that planned exhibits and educational displays expected to open next year might anger Republican lawmakers—who share control of the agency’s budget—or a potential Trump administration.

She was tapped for the job at a sensitive time for the agency—days before federal agents searched former President Donald Trump ’s Mar-a-Lago resort in 2022, spurred by the Archives’ discovery that Trump had taken home classified records. Republicans accused the agency of abusing its authority and targeting the former president. GOP lawmakers grilled Shogan about alleged partisan leanings during her confirmation hearings.

Shogan has since overseen a host of changes to exhibits planned in a roughly $40 million makeover of the National Archives Museum, which draws more than a million visitors a year, and the adjacent Discovery Center, which provides education programs for students and families. Longtime employees said Shogan’s directives amounted to censorship.

Shogan’s senior aides ordered that a proposed image of Civil Rights leader Martin Luther King Jr. be cut from a planned “Step Into History” photo booth in the Discovery Center. The booth will give visitors a chance to take photos of themselves superimposed alongside historic figures. The aides also ordered the removal of labor-union pioneer Dolores Huerta and Minnie Spotted-Wolf , the first Native American woman to join the Marine Corps, from the photo booth, according to current and former employees and agency documents.

The aides proposed using instead images of former President Richard Nixon greeting Elvis Presley and former President Ronald Reagan with baseball player Cal Ripken Jr.

After reviewing plans for an exhibit about the nation’s Westward expansion, Shogan asked one staffer, Why is it so much about Indians? according to current and former employees. Among the records Shogan ordered cut from the exhibit were several treaties signed by Native American tribes ceding their lands to the U.S. government, according to the employees and documents.

For an exhibit about patents that had changed the world, Shogan directed that the patent for the contraceptive pill be replaced. Aides substituted the patent for television. During discussions about what to use instead of the birth-control pill, an aide to Shogan suggested a patent for the bump stock, a device that allows a semiautomatic weapon to operate as a machine gun, according to two former employees.

Shogan and her top advisers told employees to remove Dorothea Lange ’s photos of Japanese-American incarceration camps from a planned exhibit because the images were too negative and controversial, according to documents and current and former employees. Shogan’s aides also asked staff to eliminate references about the wartime incarceration from some educational materials, other current and former employees said.

Ellis Brachman , a senior adviser to Shogan, complained to some employees that they were too woke, according to current and former employees.

The National Archives declined to make Shogan available for an interview. It responded on her behalf with a statement that said the agency was committed to operating without ideology or partisanship. “Leading a nonpartisan agency during an era of political polarization is not for the faint of heart,” the statement said.

This account is based on interviews with nearly a dozen current and former Archives employees, as well as internal documents and contemporaneous notes reviewed by The Wall Street Journal.

At least a half-dozen senior officials have stepped down in recent months, some blaming Shogan’s leadership. One longtime Archives employee filed a federal whistleblower complaint this summer, alleging Shogan abused her authority and engaged in censorship. The U.S. Office of Special Counsel declined to move forward, in part because the employee didn’t have enough firsthand knowledge to substantiate the claims. The office wouldn’t confirm or deny the complaint, which hasn’t been previously reported.

The Archives was thrust into the spotlight after it discovered classified documents in boxes it retrieved from Trump after he left the White House. The agency referred the matter to the Justice Department in February 2022, which led to the search of Trump’s Florida resort. The former president was indicted on federal charges last year. A judge dismissed the case this summer. The National Archives also retrieved classified documents from Biden last year after the president’s lawyers notified the agency of their discovery.

Shogan’s first Senate confirmation hearing in September 2022 came roughly six weeks after the Mar-a-Lago search. Senators at the hearings raised Shogan’s past social-media posts and a 2007 academic article she published, saying they revealed liberal leanings that disqualified her from stewardship of the country’s most valued historical documents.

They warned that they would be watching closely for signs that she was pulling the independent agency to the left.

“You’re an extreme partisan and your record shows that,” Sen. Josh Hawley (R., Mo.) said.

“I stand by my record of nonpartisan service,” Shogan told them.

‘Harmful content’

The National Archives, created by Congress in 1934, houses 13.5 billion pages of paper records, more than 33 billion electronic records and tens of millions of photos, maps and other items. The Declaration of Independence, Constitution and Bill of Rights sit in the museum’s rotunda.

Last year, the agency began what it described as a once-in-a-generation redesign of its permanent galleries and Discovery Center. Plans for the project began years before Shogan was sworn in as the country’s 11th archivist and the first female in the role.

Shogan had previously worked as senior vice president of the White House Historical Association and for the Library of Congress. She has a doctorate in American politics from Yale University. Campaign-finance reports show she donated to the Democratic presidential campaigns of Hillary Clinton and Barack Obama .

Past archivists often spanned administrations of both parties. Shogan’s predecessor, David Ferriero , was nominated by former President Obama in 2009 and served until retiring in 2022.

The Senate Homeland Security and Government Affairs Committee initially deadlocked on Shogan’s nomination. But she later advanced to the full Senate, which confirmed her in May 2023. Hawley and most other Republicans voted against her .

Soon into her tenure, one complaint aired by Republicans during her confirmation hearings was answered. In 2021, the agency had put a banner atop its online catalog that warned about “potentially harmful content,” a recommendation of an internal task force on racism convened by Shogan’s predecessor. Archives records include documents with offensive, discriminatory or graphic language and images. The banner annoyed Republicans, including Sen. James Lankford (R., Okla.), who accused the agency of trying to “ cancel ” America’s founding documents.

Three months after Shogan stepped into the job, the banner was gone. A spokeswoman for Lankford said last week, “While no one denies the darker chapters of our history, labeling the founding documents as harmful was wrong and Sen. Lankford is glad the banner was removed.”

In the summer of 2023, during planning for an exhibit on coal communities featuring images by photographer Russell Lee from the 1940s, Brachman—Shogan’s senior adviser—requested changes to the accompanying text. Instead of saying that coal companies recruited workers from plantations, Brachman asked to identify the recruits as Southern farmworkers, according to former employees and documents.

Archives employees complained, and a compromise was struck. The coal workers would be identified as “Black sharecroppers from the American South.”

Brachman also asked to cut references to the environmental hazards caused by the mining industry, according to the employees and documents. Brachman declined to comment. That exhibit opened in March.

Last fall, as employees began soliciting bids to build the exhibits for the renovation, Shogan told senior officials she wanted sweeping changes to the plans and that she wanted staff to make sure the exhibits weren’t pushing a partisan agenda, according to former employees.

Senior archives leaders repeatedly told employees that museum exhibits needed to be relatable for the average visitor, including Iowa farmers. One former staffer was told to look for success stories about white people, according to current and former employees.

“To be successful, it is imperative that the National Archives welcomes—and feels welcoming to—all Americans,” the agency said in its statement.

King to king

Shogan’s aides offered several explanations for removing the photograph of Dr. King and adding one of Nixon clasping hands with Elvis. One was a reluctance to feature activists. Senior officials also raised concerns that visitors might not recognize King, and they said there were too many other people in the photo, current and former staff said.

The senior officials rejected alternative photos of King, the staffers said.

Plans for a gallery called “Your Archives in Action” included an example of how public records had been used to return assets to Jews after the Holocaust. Brachman told employees that he was Jewish, but the Holocaust story needed to go, former employees said. They interpreted the order as part of Shogan’s efforts to focus on lighter moments in U.S. history.

A proposed exhibit exploring changes to the Constitution since 1787, which included amendments abolishing slavery and expanding the right to vote, was shrunk. Archives leaders told employees that focusing on the amendments portrayed the Founding Fathers in a negative light, by highlighting issues they had gotten wrong, according to current and former employees.

Shogan’s team also asked that a video promoting National History Day remove a photo of former first lady Betty Ford wearing an Equal Rights Amendment pin, according to former employees.

The Archives said in its statement that Shogan was “working to ensure the agency tells a more complete story of American history,” pointing to her decision to add the Emancipation Proclamation and the 19th Amendment, which granted women the right to vote, to the museum rotunda.

Shogan’s changes have delayed the opening of new exhibits, initially set for next summer, and are expected to add at least $332,000 to costs, documents show.

The agency is facing a budget shortfall, and there are fears of funding cuts ahead. Trump and his allies in Congress have said they plan to slash funding for many federal agencies and weed out alleged instances of progressive leanings throughout the executive branch.

Archives employees say Shogan has gone out of her way to appease Republicans, including giving a two-week internship to the niece of Texas Republican Rep. Pete Sessions , a critic of the agency.

Shogan invited former first lady Melania Trump to speak last December at a naturalization ceremony at the Archives. Shogan for weeks resisted warnings from employees that she needed to give notice to the White House, especially since the event came shortly before the Iowa caucuses. White House officials were surprised when Shogan finally told them, given the agency’s legal entanglement with the former president.

At the naturalization ceremony, Shogan presented the former first lady with framed side-by-side copies of the conviction record of Susan B. Anthony —who was arrested for casting a ballot before women had the right to vote—as well as Trump’s presidential pardon of Anthony. A spokeswoman for the former first lady didn’t respond to a request for comment.

Shogan last week spoke at a closed-door event at the Archives called “Faith in America,” hosted by Stand Together, a nonprofit group founded by libertarian billionaire Charles Koch . Shogan’s husband, Rob Raffety , is Stand Together’s internal communications director. He declined to comment. The event didn’t appear on the Archives’ public calendar.

Among the points Shogan addressed during her welcome remarks at the private gathering: the importance of using America’s founding documents to teach and inspire.

Write to Andrew Restuccia at andrew.restuccia@wsj.com and Rebecca Ballhaus at rebecca.ballhaus@wsj.com