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.

Determining the fees that you pay is not simple. Fees can be charged for plan administration, investments and sometimes for individual services provided to participants; all 401(k) plans are required to send an annual notice that explains the fees that can be deducted from your account, but understanding them is another matter.

“It’s very difficult for people to understand their fees unless they’re investment professionals, which most retirees are not,” said Lisa M. Gomez, assistant secretary for employee benefits security at the U.S. Department of Labor.

The Secure 2.0 legislation of 2022 directed the department to examine ways to improve plan information, including how to understand fees. It expects to report to Congress with recommendations by the end of 2025, Ms. Gomez said. The department publishes a guide to 401(k) fees and has a toll-free line with advisers who can help participants understand their fees (866-444-3272).

But asking your employer about fees is a good starting point. “You have the right to know what you’re paying, so go to your human resources department, and ask them to tell you about your options and what they cost,” Mr. Puritz, the managing director at Rebalance, said. The Financial Industry Regulatory Authority offers an online tool that analyzes how fees and other expenses affect the value of mutual funds and exchange-traded funds over time.

Your plan is mediocre. What now?

If your employer’s plan offers an annual matching contribution, save enough to capture it — doing otherwise leaves money on the table. “If they are matching dollar for dollar or 50 cents on the dollar, that’s a 100 percent or 50 percent return with almost zero risk,” said Heath Biller, a financial planner with Fiduciary Financial Advisors in Grand Rapids, Mich.

Pay careful attention to your investment choices, and look for the least expensive options. If possible, find a low-cost index fund that tracks the entire stock market. “Even if the investment menu is larded with high-expense funds, you may be able to find an index fund or a decent quality target date fund series,” said Christine Benz, director of personal finance and retirement planning at Morningstar.

You can also push for change. Mediocre 401(k) plans can get better. Employers are usually the fiduciary with a legal responsibility to consider only the interest of participants, and it’s in their own best interest to take your misgivings under consideration. “You can raise your concerns about high fees or poor investment options with your employer and ask if the company is able to consider adjustments,” Mr. Biller said.

After you’ve captured the employer match, consider low-cost options outside your 401(k) for additional saving. This year, you can contribute up to $23,000 to a 401(k) and $7,000 to an I.R.A.; savers 50 and older can contribute more via catch-up contributions. Eligibility to deduct the I.R.A. contributions phases out at certain income levels. Establishing one low-cost I.R.A. also lets you roll balances over to a single account as you change jobs through the course of your career, which is a great way to stay organized.

If you have self-employment income in addition to wages, a Simplified Employee Pension I.R.A. or Solo 401(k) offer routes around the I.R.A. contribution limits. Solo 401(k) accounts have higher contribution limits and are not available if you operate a company with employees; the government reporting requirements vary between these two options.

Yulia Petrovsky, a financial planner in San Francisco, has many clients working for large technology companies who also have side businesses. “Some of them are doing start-up work,” she said. “Some have marketing or other consulting gigs, especially when in between jobs, so these accounts can be a real slam dunk.”

Taxable investment accounts offer another route around I.R.A. contribution limits, especially for older retirement savers. Unlike 401(k) and I.R.A. accounts, they don’t come with an upfront tax benefit. Investment gains are subject to capital gains rates, although these are more favorable than ordinary income tax rates imposed on withdrawal from tax-deferred accounts.

Tax deferral is less important for older investors, who have less time to benefit from the tax-deferred compounding available in such accounts than younger investors.

It’s also possible to use tax-efficient investments in taxable accounts, such as broad-market equity exchange-traded funds, which have become very tax efficient, and municipal bonds — which generally are not subject to federal income taxes — for fixed income, Ms. Benz added.

“It’s not that difficult to simulate some of the tax-sheltering characteristics of a tax-deferred account in a taxable account,” she said.