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Payroll & HCM Services for Nonprofits

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Why Does Your Nonprofit Need a Payroll & HCM Service Provider?

Establishing and launching a successful nonprofit is demanding enough without adding payroll, tax, compliance, and workforce management tasks as an in-house burden. Equally important, inaccuracies or errors in these processes could lead to employee retention issues, financial/legal penalties, or significantly detract from pursuing your mission and vision. Whether you’re leading a charitable organization, university, church, or political organization, a number of tax obligations and considerations apply.

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IRIS Payroll & HCM Service Benefits

IRIS Payroll & HCM Services is specifically designed to support our clients in the nonprofit industries, minimizing manual tasks and alleviating tax, payroll, and compliance concerns.

Here’s how IRIS Payroll & HCM Services can help your business:

  • Reduce involvement in payroll administration.
  • Improve efficiency by outsourcing non-revenue processes.
  • Ensure accurate and timely employee payments.
  • Automatically calculate, deduct, and pay all payroll taxes.
  • Identify and claim eligible tax credits.
  • Integrate payroll with timekeeping, benefits, onboarding, and workforce management.
  • Handle IRS inquiries, manage SUI, and file taxes with appropriate agencies.
  • Payroll Processing

    Given that a nonprofit’s workforce can encompass employees, board members, executives, and volunteers, managing payroll and correctly classifying each role can be quite challenging. This complexity is further increased by the diverse funding sources that nonprofits often use, such as grants, fundraising events, crowdfunding, and private or corporate donations. To avoid legal issues, payroll mistakes, delays in payment, or incorrect tax calculations, it is crucial to understand the appropriate payment methods for the various types of workers in a nonprofit.

  • Paying Executives and Board Members

    According to the IRS, board members and executives should receive “reasonable compensation” similar to what they would earn at a comparable organization. Compensation can include wages, benefits, perks, and bonuses. Executive and board compensation often reaches six figures, influenced by factors such as educational background, experience, local compensation averages, job responsibilities, hours worked, and the nonprofit’s total budget.

  • Paying Volunteers

    Volunteers play a crucial role in advancing a nonprofit’s mission by offering their time for unpaid projects or tasks. To encourage volunteerism, many nonprofits provide incentives like discounts, expense reimbursements, or stipends. However, it’s essential to note that stipends and similar benefits are often considered taxable income, subject to income tax and FICA contributions. Some small perks can be excluded from taxable income, but always consult payroll experts to stay within FLSA guidelines. Volunteers earning less than $500 annually might be protected from tort liability under the Volunteer Protection Act. Keeping these tax and liability concerns in mind is vital for managing your nonprofit’s workforce and compliance strategy.

  • Paying Ministers and Religious Figures

    Since churches and religious organizations are unique 501(c)(3) entities, payroll for ministers and religious figures differs from other nonprofit roles. Ministers are often employees, though some may be classified as self-employed for Social Security and Medicare tax purposes if they seek a tax exemption from the IRS by filing Form 4361. Employee ministers’ pay is subject to income tax, and churches are generally exempt from the employer portion of FICA taxes for ministers. Any compensation, including housing stipends, must be reported appropriately for tax purposes. Housing stipends are excluded from gross income for federal income tax purposes but are subject to self-employment tax. IRIS payroll & HCM provides specialized payroll and compliance support for these organizations.

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Contact us today so you can focus on what really matters—dedicating more time to your mission.

Resources for Nonprofit Organizations

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Gene D Huber, CFO

“I can always count on timely and accurate information.  Also, IRIS is very responsive and helpful when I have questions or concerns.  They are all very knowledgeable and friendly.”

Get in touch

Stop worrying about getting your payroll done right and let our comprehensive payroll & HCM solutions revolutionize your nonprofit. Take the first step toward stress-free payroll & HCM today.

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Frequently Asked Questions

Can I use grants to pay nonprofit employees?

Funding from grants is eligible for use to cover the overall expenses of a grant-approved project, which includes payment to employees or payroll-related expenses. When grant funding is used to pay employees, each employee must diligently track their hours, activities, and completed work to demonstrate total time spent and the work’s relevancy to the grant-funded project. This process is greatly simplified with the use of leading-edge payroll and time and attendance software.

Are nonprofits exempt from payroll taxes?

No. Most nonprofits must withhold and deposit funds to pay FICA (Social Security and Medicare) taxes on each employee’s behalf and complete tax returns accurately. In some cases, a nonprofit may also be obligated to pay state unemployment taxes or local taxes that apply to the jurisdiction where it operates.

How could my nonprofit lose its tax-exempt status?

A 501(c)(3) nonprofit could lose its tax-exempt status if it fails to submit Form 990 or pursues activities that either deviate from tax-exempt activities or benefit a private interest. For certain organizations, tax-exempt status could be rescinded for lobbying activities or participation in a political campaign.

Lastly, if a disproportionate amount of a nonprofit’s income is derived from activities that are not related to its mission, tax-exempt status could also be withdrawn.

Do I need to file a tax return as a nonprofit?

A nonprofit must submit a yearly information return, Form 990, which details the organization’s income, activities, and expenses. This must be submitted in less than six months after the end of the organization’s fiscal year. Various permutations of Form 990 exist to align with an organization’s classification and activities, so it’s best to work with one of CAVU’s payroll guides to support the process and ensure accurate completion of Form 990 and other IRS-required documents.