Beth Crowell was proud to work for the Internal Revenue Service.

She had spent much of her career as an accountant for large corporations, gaining intimate knowledge about how they do — and sometimes don’t — pay the taxes they owe. Working for the I.R.S. in Colorado, she hoped to put her skills to a new use. She wanted to help collect more money for the federal government.

Not long after joining last July, she had her chance. Ms. Crowell, 64, joined a team that had started an audit of a company earning roughly $3 billion a year. The I.R.S. had never examined the firm before, Ms. Crowell said, because the agency hadn’t had enough employees with the skills for such complex cases. “They’re a large multinational company, and it is not a normal thing to not have been examined,” she said, declining to name the firm.

By hiring Ms. Crowell and thousands of other experienced tax professionals like her last year, the I.R.S. was trying to fill those gaps and rebuild its ability to enforce tax laws after years of decay. The effort was expected to help the United States recoup billions in additional tax revenue.

Then the layoffs started. With Trump administration targeting recent hires across the government, the terminations hit particularly hard in Ms. Crowell’s division, large business and international. Of the more than 7,000 people laid off from the I.R.S. so far, roughly half worked in her department.

As a result, the I.R.S. may struggle even more with its basic mission of collecting taxes. Work-intensive investigations into large businesses and rich Americans could decline, a drop in enforcement that would add to the deficit even as Elon Musk says his team is helping narrow it.

The audit Ms. Crowell was in the middle of conducting is now adrift. Five of the nine people working on it, including Ms. Crowell, were laid off. What she called a slam-dunk case for the I.R.S. may not be finished.

“We were going to work through these issues and have it done in an effective professional and collaborative manner,” she said. “All of the momentum we had is gone. I’m not sure they’re going to be positioned and have the support they need to restructure and reconvene to overcome all of this.”

Firing probationary employees like Ms. Crowell was just the beginning of President Trump’s far-reaching agenda for the I.R.S. The administration is preparing budget cuts and further layoffs that could ultimately force the I.R.S. to shed as much as half of its 100,000-person work force — a drastic reduction that could mean many Americans face less scrutiny, and receive less help, on their taxes. At the same time, Mr. Trump is asserting more political control over an agency that has historically been insulated from changes in leadership at the White House.

Soon after the election, Mr. Trump chose Billy Long, a former Republican congressman and vocal supporter of the president, to lead the I.R.S. The choice of Mr. Long was unusual. He’d never run a large organization and his only background in tax consisted of pitching small businesses on a fraud-riddled tax credit. And by deciding to replace Daniel Werfel, then the head of I.R.S., years before the end of his term in 2027, Mr. Trump was upending the norm that commissioners of the I.R.S. stay in the role even as a new president comes into office.

Mr. Musk, who claimed to hold the record for the largest tax bill for an individual after having paid more than $11 billion to the I.R.S. in 2021, has dispatched technologists to the agency with the goal of automating many of its functions. The presence of the so-called Department of Government Efficiency is growing at the I.R.S., where Mr. Musk’s allies are preparing to cancel scores of contracts with outside technology vendors.

And with homeland security officials already asking for the I.R.S. to help with deporting immigrants, some agency officials and tax experts also worry that the Trump administration could try to use vast stores of taxpayer information to execute political goals.

This article is based on interviews with more than a dozen current and former I.R.S. officials, aides on Capitol Hill and others in Washington who closely follow the tax agency. They described deep uncertainty as the I.R.S. cycled through three leaders in a matter of weeks and Mr. Trump’s team moved to rapidly remake one of the government’s most fundamental agencies.

An I.R.S. spokeswoman declined to comment. A Treasury spokesperson said the Trump administration was exploring different options for streamlining the I.R.S.

“While no plan has been approved to date, modernization is necessary to keep up with the process by which Americans file their taxes, including the reality that over 90 percent of individual tax returns are filed electronically,” the spokesperson said. “These changes are aimed at improving taxpayer customer service and ensuring a smooth and successful filing season.”

‘Uncharted Situation’

Even with his successor picked, Mr. Werfel, a Biden appointee, had wanted to stay in his job for as long as possible.

While the generational overhaul of the I.R.S. he was hired to lead was now under threat by Mr. Trump, Mr. Werfel thought he might still be able to stay on for the first few months of the Trump administration. Mr. Long’s Senate confirmation would take time, and Mr. Werfel wanted to help the I.R.S. get through filing season, its most high-stakes period when millions of Americans file their returns.

Throughout the transition, Mr. Werfel repeatedly asked members of incoming Treasury Secretary Scott Bessent’s staff whether they would want him to keep working. But Mr. Bessent and his staff never asked Mr. Werfel to stay — nor did they explicitly tell him to go — so he decided he would resign, hoping to avoid drawing any additional attention to the I.R.S., already a target for Republicans.

“This situation would have been somewhat uncharted,” Mr. Werfel said in an interview before he stepped down on Jan. 20. “I wasn’t able to predict what this uncharted situation would entail, and all of this would be happening while the I.R.S. has some important obligations in the medium term.”

As the agency responsible for taking money from Americans to fund the government, the I.R.S. has long been unpopular with the public. In that sense, it was a natural target for an antigovernment crusade, even if it could mean bringing in less tax revenue. Mr. Musk, Mr. Long and members of Mr. Trump’s staff have even raised the possibility of abolishing the I.R.S. altogether.

Even before Mr. Trump took office, associates of Mr. Musk were scrutinizing the I.R.S., asking about the agency’s information technology and head count during transition meetings. The I.R.S., under its modernization plan, had been working to update its rickety technology systems — but the Trump team quickly made clear that it believed the agency was moving far too slowly and employed far too many people.

When he arrived at I.R.S. headquarters in February, Gavin Kliger, a 25-year-old software engineer on Mr. Musk’s DOGE team, wanted broad visibility into the agency’s databases, which are full of personal information about Americans’ jobs, earnings and families. While I.R.S. officials agreed to eventually let him see anonymized tax data, a court order barring DOGE employees from Treasury systems has so far prevented Mr. Kliger from actually doing so.

In meetings, Mr. Kliger, who wears all-black clothing, has often been impatient, accusing officials of stonewalling him and disobeying White House executive orders when they raised legal concerns with his requests, according to people who have interacted with him. Mr. Kliger did not respond to a request for comment.

When I.R.S. human resources staff did not spend a weekend readying the agency to host another DOGE aide, Sam Corcos — a technology entrepreneur and a self-described minimalist who has repeatedly said he only owns one pair of pants — Mr. Kliger blamed the chief human capital officer at the I.R.S. for not moving quickly enough.

A new I.R.S. chief, promoted under the Trump administration to temporarily lead the agency, agreed. Melanie Krause had taken over after the last interim leader, Douglas O’Donnell, retired. Last week, she put the chief human capital officer, Traci DiMartini, on administrative leave for not accommodating DOGE requests and her performance during the first round of mass layoffs, according to two people familiar with the matter.

‘My Taxpayer Dollars Were Wasted’

Caryn Burns had long been frustrated with the I.R.S. It took too long to get a call back, and the I.R.S. staff she dealt with over the course of her career as an accountant could be underwhelming. But when she started working there herself in September, she started to get a sense of why the agency so often seemed to fall short.

The technology was archaic and took to weeks to learn to use. And while the work force was growing rapidly under the Biden administration — with the number of employees rising by 20,000 over three years — Ms. Burns said the I.R.S. still seemed short of staff.

“They couldn’t hire people quick enough to start making the necessary changes,” she said. “Once I learned all of this and once I started and I had access to all these programs, I realized this isn’t what I thought it was. There really aren’t a lot of people there.”

Ms. Burns, 58, had also worked in the large business and international division, in the Phoenix, Ariz., area, before she was laid off last month. She said she was close to completing an audit that would have generated a significant tax payment to the I.R.S. She’s not sure if her former colleagues will have the resources to finish it after the layoffs.

“I voted for Trump; I do like Trump,” she said. “I like what he did the last term in office and all of the things he stood for.”

“But now that he’s brought in Elon Musk,” it’s a mess, she said.

I.R.S. leaders had scrambled to identify all of their probationary employees, whom the Trump administration had directed should be laid off. It was a struggle to quickly put together the list; employees deemed necessary for filing season, for example, were supposed to be spared. The day before the firings started, several top officials at I.R.S. headquarters were not sure exactly how many people the agency would ultimately let go.

Amanda Musgrave, 41, showed up to work expecting to be laid off quickly. She had started working at the massive I.R.S. campus in Austin, Texas, last June, so she knew she was vulnerable. Mrs. Musgrave had enjoyed the job and was frustrated that it had to end.

Even with security officers and human resources staff on campus to facilitate the layoffs, Mrs. Musgrave said she and some of her colleagues waited for hours for the official termination notice to arrive in their email inboxes. The stress started to build, and she eventually she got tired of waiting. In the afternoon, she demanded that her manager just fire her so she could go home.

“I ended up having a panic attack, and that was not fair,” she said. “It was completely degrading and disgusting what I went through.”

More broadly, Mrs. Musgrave has a lingering feeling that the layoffs directed by Mr. Musk’s team would create more government waste — not reduce it. Not only might Americans find it easier to avoid paying all of the taxes they owe, but all of the time and money the I.R.S. spent on hiring her and thousands of others were ultimately for nothing.

“I’m appalled my tax dollars were wasted on getting all those employees trained, and they didn’t even get the chance to get out of their probationary period,” she said.