What to expect from nonprofit payroll services

by | May 30, 2023

Managing payroll for nonprofit organizations comes with unique requirements and considerations. Ensuring that your nonprofit payroll services are up to the task of withholding payroll taxes, complying with grant regulations, and ensuring compliance and transparency can be a huge lift. 

Finding the right person or organization to handle the monumental task of payroll services will enable you to rest easy knowing that this task is in good hands and that your employees and donors are confident and happy with the results. 

In this article, we will explore the distinct payroll requirements for nonprofits. Understanding these nuances will help your organization effectively manage its payroll processes and avoid potential pitfalls.

Unique Payroll Requirements for Nonprofits

Withholding Payroll Taxes

While nonprofit organizations are generally exempt from federal income tax, they still have payroll tax obligations as it relates to their employees. Nonprofits must withhold and remit payroll taxes on behalf of their employees, including federal income tax, Social Security, and Medicare taxes in order to remain compliant with tax regulations. 

Using Grants to Pay Employees

Organizations often rely on grant funding to support them in carrying out their mission. Sometimes portions of these grants are awarded specifically for personnel costs, or can be allocated to those if employees are directly working on the grant-related projects. In these scenarios, it is cruel to effectively track, document, and allocate timesheets and grant-funded payroll separately to ensure transparency, accuracy and responsible use of grant funds.

Reviewing Executive Salaries

Nonprofit organizations must carefully manage executive compensation to maintain public trust and meet the legal requirement of the IRS to pay executives a “reasonable” salary. Organizations should establish a formal process for reviewing and determining the executive salary based on industry benchmarks.

Minister Pay

In religious or faith-based organizations, paying ministers and clergy involves specific considerations as well. They may often be classified as self-employed for tax purposes. However, the organization may still be required to report compensation and file appropriate forms depending on circumstances. 

Form 990

Filing your annual information return can be a huge undertaking and also requires the completion of important payroll details from throughout the year including payroll expenses, employee benefits and executive compensation. Accurate and thorough completion of Form 990 is crucial for nonprofits to maintain their tax-exempt status and showcase their commitment to transparency and accountability.

Common Mistakes and Problems

Processing Errors

Misclassifying Employees

Understanding employee classifications (as an ‘employee’ or ‘contactor’ and further either ‘exempt’ or ‘nonexempt’), at both the federal and state levels, can be a confusing issue that can have serious legal and financial implications. According to the council of nonprofits, misclassifying a worker can result in the nonprofit owing significant penalties, back taxes, and backpay. 

Miscalculating Payroll

Mistakes in calculating payroll can result in underpayment or overpayment of employees, leading to dissatisfaction and potential legal issues. Implementing a reliable payroll software and ensuring your payroll service provider is an expert in nonprofit payroll can help to mitigate such errors and avoid costly mistakes. 

Missing Payroll Deadlines

This can have significant consequences, such as delayed payments to employees or non-compliance with tax regulations. Nonprofits must adhere to strict timelines for processing, remitting and providing the necessary payroll documentation to employees. 

Should my organization outsource payroll?

Outsourcing payroll can be an incredible relief to an organization as the burden of understanding all the nuances of this process is large. However, the additional layers of compliance, reporting, and allocations that nonprofits must adhere to makes the task even that much more complicated. When considering the prospect of outsourcing, ensure that you are working with a service that understands the intricacies of a nonprofit organization and will be on top of your compliance, reporting and payroll needs. Keep in mind what services you will need and what will be the most helpful support for your organization. Many services can complete a number of tasks including:

  • Recording employee timesheets
  • Performing payroll tax calculations on wages, vacation pay, termination pay, and banked time
  • Calculating organizational filings
  • Withholding employee deductions and making remittances to the government
  • Processing direct deposits of checks
  • Submitting employee tax forms
  • Preparing payroll journal entries

Overall, be aware that payroll management for nonprofit organizations requires careful attention to detail and thorough understanding of the specific requirements applicable to the sector. Charity CFO has experts that can help navigate the intricacies of nonprofit payroll and ensure that your organization is properly withholding payroll taxes, effectively utilizing grants for employee compensation, conducting comprehensive reviews of executive salaries, adhering to regulations concerning minister pay, and accurately completing your Form 990. 

This process helps ensure compliance, maintain transparency and demonstrate responsible stewardship of resources. By implementing best practices and seeking professional guidance when needed, non-profit organizations can streamline their payroll processes and focus on advancing their missions while remaining compliant with relevant legislative and regulatory obligations.


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