Over the course of a career, the high fees and a lower-quality menu of investment options found in some plans can shrink your balance significantly.

Chris Gentry is meticulous about his craft — he’s a professional woodworker at a small company in Brooklyn, N.Y., that makes custom dining and coffee tables, cabinets and interiors.

He creates pieces on his own from start to finish and enjoys that freedom. “It’s nice to have control over the way something should be done,” he said.

Mr. Gentry, 36, is equally conscientious about saving for retirement. He has contributed the maximum allowable amounts to his employer’s 401(k) plan over the past two years and also topped out a Roth individual retirement account. He hopes to buy an apartment and start a family soon with his partner. “It seems like all that will be expensive, so I’m trying to get an early start on retirement savings while I can,” he said. Between the two accounts, he has managed to save $80,000.

His employer kicks in a generous 5 percent of his salary to the 401(k) no matter how much Mr. Gentry contributes. But he worries about the plan’s high-cost mutual funds. “They’re expensive compared with what I can get in the I.R.A.,” he said. He even wonders if he should contribute to the plan at all. “I’m not sure how to determine at what point the fees become so expensive that the benefits of the 401(k) are outweighed by the fees.”

Fees are one of the most important factors of successful retirement investing. They determine how much ends up in your pocket after mutual funds and 401(k) plan providers take their cut. The bite especially hurts younger workers, who face the risk that high fees will compound over time.

“Fees compound in the same way that returns compound,” said Scott Puritz managing director at Rebalance, a firm that often works with clients on 401(k) rollovers and advises companies on ways to improve their plans. “People are numb to the differences, but it’s a major determinant of long-term returns.”

Costs are usually much higher in plans sponsored by small businesses, like the 10-person firm where Mr. Gentry works. His plan doesn’t offer low-cost passive index fund choices. He is invested solely in a target date fund made up of actively managed mutual funds that have lagged the overall market’s returns during the past decade. The fund charges an annual expense fee of just over 1 percent.

That amount is typical for small plans, according to data compiled for the 401(k) Averages Book, which surveys companies that provide plans to employers. For example, the survey shows that among plans with 10 participants and $1 million in assets, average investment costs are 1.10 percent. At larger firms, those fees are far lower: At companies with 1,000 to 5,000 plan participants, target date fund fees average just 0.33 percent, according to data compiled by the Investment Company Institute and BrightScope. (Target date funds shift gradually toward bonds from stocks as a worker approaches an expected date for retirement.)

It’s not unusual for small plans to carry total expenses far higher. “We often see plans that charge 2 or 3 percent all in — sometimes more,” Mr. Puritz said.

A key reason for the varying amount of fees is the fixed costs of administering a plan and how those costs are spread across companies of different sizes. “If I have a small coffee shop plan with $100,000 in assets, the costs are spread across fewer people compared with a very large company,” said Joe Valletta, principal with Pension Data Source, which publishes the 401(k) Averages Book. “The big plan has higher fixed costs, but it’s spread over a lot more employees and a larger asset base.”

Mr. Gentry is fortunate to work for an employer that offers any kind of plan. Only about half of private-sector U.S. workers are covered by an employer retirement plan at any given time, and the gap is driven by lower participation in the system by small employers, according to the Center for Retirement Research at Boston College. Workers often gain and lose coverage as they change jobs.

The coverage gap helps explain why many workers reach retirement with savings unlikely to last the rest of their lives. According to the Federal Reserve, the median retirement account holdings for workers aged 55 to 64 years old was $185,000 in 2022.

But fees also play a leading role, especially for young workers who face the compound effects over many years of saving. The difference in account balances when they retire can be staggering.

The New York Times worked with Rebalance to create a hypothetical example, illustrating the career-long effect of plans with a variety of fee levels.

We considered a 28-year-old worker with a starting salary of $75,000 who saves diligently in her 401(k) account throughout her career. She contributes 6 percent of her salary annually and receives a 3 percent matching contribution from her employer. The scenario shows the effect of what she will have at three possible retirement ages. At 65, her portfolio is nearly 66 percent smaller in a high-cost plan compared with the lowest.