Payroll for Nonprofits: An Easy Guide for Employers
Charlette has over 10 years of experience in accounting and finance and 2 years of partnering with HR leaders on freelance projects. She uses this extensive experience to answer your questions about payroll.
Heather is a staff writer and payroll specialist with several years of experience working directly with small business owners. Her expertise allows her to deliver the best answers to your questions about payroll.
This article is part of a larger series on How to Do Payroll.
Generally, nonprofits process payroll in much the same way that for-profit businesses do; however, there are some differences depending on your organization’s structure and the types of workers you need to pay. Like for-profits, all nonprofits must pay and withhold Federal Insurance Contributions Act (FICA) taxes, but 501(c)(3)s are exempt from paying federal unemployment taxes (FUTA).
You may want to use payroll software or service to manage your tax withholdings and payments; many providers offer discounted rates to nonprofits. We suggest you consider Gusto, as its small business payroll software ensures that all local, state, and federal payroll taxes are calculated, filed, and paid automatically. Plus, it offers an unlimited number of pay runs. Get started for free today.
How Payroll for Nonprofits Works
If your nonprofit has tax-exempt status (not all do), you must pay FICA taxes and withhold federal and state income tax from employee paychecks. There are many different types of nonprofits, but the most common is the 501(c)(3) organization. 501(c)(3)s are nonprofits that the IRS has recognized as tax-exempt charitable programs. Organizations with a 501(c)(3) status don’t have to pay FUTA, and state unemployment taxes (SUTA) can be paid in advance or after claims are filed.
To be considered a 501(c)(3), your nonprofit must fit into one of these categories per the IRS:
- Charitable
- Religious
- Educational
- Scientific
- Literary
- Testing for public safety
- Fostering national or international amateur sports competition
- Child or animal cruelty prevention
Nonprofits must be careful when paying workers. There’s a difference between employees, contractors, volunteers, and board members. The IRS will only allow you to make nominal payments to volunteers—anything more than that will be taxable to both you and your volunteers, and any board members who are compensated must be paid a reasonable amount per a special IRS test.
Payroll Taxes & Withholding for Nonprofit Organizations
Payroll taxes like FUTA and SUTA are handled differently within some nonprofit organizations, but let’s look at all of the payroll taxes together. Even though many nonprofits are exempt from FUTA taxes, calculating, paying, and filing the other payroll taxes accurately and on time can be a major challenge.
Here are the payroll taxes nonprofits are generally subject to pay or withhold from employee paychecks:
- FICA: Social Security and Medicare taxes, 6.2% and 1.45%, respectively, make up FICA taxes; you pay 7.65% from your bank account and withhold the same from your employees’ wages.
- FUTA: You pay FUTA taxes on the first $7,000 of each employee’s wages at a rate of 6%. This is to cover unemployment benefits for employees in the event of their termination. Employees are not responsible for paying this tax; 501(c)(3)s are exempt.
- SUTA: SUTA tax rates can vary from 2.7% to 3.4% and can sometimes be even higher for new employers that don’t have a claim history. Nonprofits can pay into the tax fund regularly or reimburse the state when former employees make claims.
- Federal income tax: You should collect a Form W-4 when your new employee is hired; it will show all of the allowances claimed so you can withhold the proper amount for federal taxes each period.
- State income tax: You may have to withhold state income taxes if your state requires it and the employee is not exempt. If your nonprofit is in a state like Florida or Texas, you don’t have to withhold state income taxes.
- Local income tax: Some localities, like New York City, charge their own tax outside of the state income tax. You will need to check your state and local laws to verify how much you need to withhold.
- Workers’ compensation: Nonprofits are required to comply with state workers’ comp laws. This ensures that your organization is covered if an employee suffers injury or death as a result of work performed on the job. Rates depend on position, claim history, and other factors. Many payroll services offer pay-as-you-go workers’ compensation coverage tied in with payroll.
Unemployment Taxes for Nonprofits
If your organization is a 501(c)(3), it’s automatically exempt from FUTA taxes. However, you are still subject to the requirements of your state unemployment tax program.
Federal law does give you the choice to opt out of paying into the state unemployment tax program and reimburse the state only for unemployment claims paid out to former employees. This could save your organization a significant amount of money if you’ve had little to no unemployment claims in the past. Many nonprofits pay more in taxes than the state pays for its claims.
A major disadvantage to choosing the reimbursement option is that you don’t know for certain how much your unemployment claims will be. It’s possible to underestimate the total claims that will be made, and you could face a large, unexpected tax bill for the period.
Pro Tip: To mitigate your risk, start tracking your annual unemployment costs. From there, set aside an adequate amount each year to cover future estimated liabilities. It’s important to remember that even employees who voluntarily terminate their employment can still be eligible for unemployment benefits.
Benefits & Other Deductions for Nonprofits
When processing payroll for your nonprofit, taxes aren’t the only consideration; health insurance benefits and other deductions must also be withheld and paid. You’re not required to offer health insurance unless you have at least 50 full-time equivalent (FTE) employees, but it could boost employee morale. You might also consider other benefit options, such as 401(k)s, commuter benefits, and dental insurance.
How to Pay Nonprofit Workers
One of the first decisions you make when doing payroll for a nonprofit is deciding how much to pay your workers. Federal law dictates that all employees must be paid a minimum wage of $7.25 an hour—but this doesn’t apply to volunteers. Commissions and bonuses should be avoided because the IRS will likely view them as red flags. They’re typically tied to performance and can open the door to fraudulent activity.
Minimum Wage for Nonprofits
The minimum wage is the lowest pay rate employers are allowed to pay their employees. Although the federal rate is $7.25 an hour, you may have to pay more, depending on the state your organization is in. Currently, 30 states and D.C. have minimum wages above the federal minimum wage.
It’s a good idea to check your state’s minimum wage before making any job offers. For minimum wage laws specific to your state, check out our state payroll directory.
Some nonprofits hire employees with disabilities, which allows them to pay a lower rate than the minimum wage law requires. You will need to request a certificate from the Department of Labor’s (DOL’s) Wage and Hour Division before implementing. You can also pay employees under the age of 20 a minimum rate of $4.25 an hour for their first 90 days of employment.
To learn about more DOL-allowed exceptions, check out our article on minimum wage exemptions.
Independent Contractors Working for Nonprofits
Independent contractors are workers who provide goods or services to an organization per a contract or other agreement. Similar to other employers, nonprofits don’t have to withhold or pay payroll taxes on payments made to independent contractors. Independent contractors will need to complete a Form W-9 with their tax identification number and other information—this makes it easy for you to report their annual earnings on a Form 1099 at the end of the year.
Be careful when classifying your workers as employees versus independent contractors. If you fail to withhold and pay taxes on amounts paid to an independent contractor and the IRS discovers that your contractor is actually an employee, you could face penalties and additional payroll taxes. Contractors generally have more control over their time, pay, and work methods than employees.
Volunteer Compensation
It’s customary for nonprofits to work with volunteers in addition to employees, but payments to volunteers are not handled the same way.
A volunteer, according to the DOL, is an “individual who volunteers or donates their services, usually on a part-time basis, for public service, religious, or humanitarian objectives, not as employees and without contemplation of pay.”
If you decide to pay a volunteer, the amount must be nominal, meaning insignificant and irregular. The DOL doesn’t consider payments over 20% of what you would pay a full-time employee to perform the same services to be nominal. Paying a volunteer a regular and significant amount can raise a red flag and result in a determination that your volunteer is an employee whose wages you should be paying taxes on.
Generally, if you’re paying a volunteer beyond a nominal amount, you should withhold income and FICA taxes in addition to paying the matching employer FICA taxes. This includes any stipends or allowances paid. Non-cash benefits, or perks, that aren’t tax-exempt must be assigned a value so you can collect and pay the proper employment taxes. Inexpensive items like T-shirts or coffee mugs can be excluded.
When you reimburse employees for purchases they can deduct on their taxes (such as required uniforms), the amount is not taxable, so you won’t have to treat it the same as wages. If you pay a volunteer with a cash payment, your organization will be required to follow the same reporting and withholding guidelines as it would for any other employee.
It’s important to mention the use of interns for nonprofit organizations. As per the DOL, students working for “for-profit” employers are entitled to minimum wages and overtime pay under the Fair Labor Standards Act (FLSA). Unpaid internships for public sector and nonprofit charitable organizations, where the intern volunteers without expectation of compensation, are generally permissible. Nonprofits must be aware of these regulations before hiring any interns on a paid or unpaid basis.
Board Members of Nonprofit Organizations
Not all nonprofits have a board of directors to manage their finances and other activities, but those that do need to ensure they are paying them properly. While the IRS doesn’t specifically state how much you can pay board members, it does state the payments must be reasonable.
Compensation for officers, directors, key employees, and others with the power to exercise substantial influence over the nonprofit should be decided by a nonbiased party.
The following are steps you can take to ensure your board members are being paid a reasonable amount:
For help comparing salaries across positions, check out the Bureau of Labor Statistics’ free salary comparison tool.
Labor Laws for Nonprofits
There are numerous labor laws that employers are expected to follow, including overtime rules, meal time laws, and paid time off policy requirements. Nonprofits are generally exempt from these when it pertains to volunteers, but it’s important to be aware of them when setting human resource policies for employees. You should also consider state-specific laws because they can differ from federal laws.
Here are some of the labor laws you should be concerned about:
Annual Reporting for Nonprofits
Many nonprofit organizations are tax-exempt; however, they are still obligated to file annual tax reports to the IRS. Some religious organizations, schools, and other nonprofits are exempt from this, but most nonprofits will need to file annually for the IRS to understand their operations and for them to maintain their tax-exempt status.
Some of the forms that you may need to file, depending on your entity, are:
- Form 990-N: Annual Electronic Filing Requirement for Small Exempt Organizations
- Form 990: Return of Organization Exempt from Income Tax
- Form 990-EZ: Short Form, Return of Organization Exempt from Income Tax
- Form 990-PF: Return of Private Foundation
Nonprofit Payroll Providers
When looking for the best nonprofit payroll providers, you don’t have to limit your search to services that only target nonprofits. General payroll software will work just as well. The differences between payroll for nonprofits versus for-profits aren’t so great that it’s necessary to use a completely different package.
Nonprofit Payroll Services | Best for | Pricing |
|---|---|---|
 | Tech-forward nonprofits with fewer than 100 employees that are looking for both payroll and HR support | Starts at $46 per month ($40 base fee plus $6 per employee) |
 | Nonprofits that already use QuickBooks for their accounting | Starts at $49 per month ($45 base fee plus $4 per employee) |
 | Nonprofits that need a robust HR solution | Starts at $104 per month (for a basic small business package $99 base fee plus $5 per employee) |
 | Nonprofits with fewer than 25 employees that need a simple payroll solution | Starts at $21 per month ($17 base fee plus $4 per employee) |
 | Nonprofits that need scalable payroll software to grow with | Starts at $68 per month ($65 base fee plus $3 per employee) for an essential plan |
Bottom Line
The most challenging part of doing payroll for a nonprofit is balancing budget and other important business decisions with compliance. There are a ton of rules and regulations that impact payroll for nonprofits. Knowing that you’re not subject to FUTA taxes or that you don’t need to pay volunteers a significant amount for their services is important for minimizing penalties and saving money.
