The Payroll Audit Checklist: Key Steps for Workers and Employers

By Manoj Sharma

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The Payroll Audit Checklist: Key Steps for Workers and Employers
The Internal Revenue Service today encouraged workers and employers to review withholding and payroll tax responsibilities ahead of National Payroll Week. Observed Sept. 7-11, National...

The Internal Revenue Service today encouraged workers and employers to review withholding and payroll tax responsibilities ahead of National Payroll Week.

Observed Sept. 7-11, National Payroll Week recognizes payroll professionals and the important role they play in helping ensure employees are paid accurately and on time. The observance also offers an opportunity for workers to look more closely at their paychecks and for employers to revisit important payroll responsibilities. 

“Payroll professionals play an essential role in supporting America’s workers, businesses, and tax system,” said IRS Chief Executive Officer Frank J. Bisignano. “During National Payroll Week, we recognize the contributions of payroll professionals and reaffirm the IRS’s commitment to providing the tools and services they need to meet their responsibilities with confidence.” 

Workers: Check withholding now

Federal income tax is generally paid throughout the year as income is earned. For employees, employers generally withhold federal income tax from each paycheck based on the employee’s earnings and the information provided on Form W-4, Employee’s Withholding Certificate.

The IRS encourages workers to check their withholding periodically, particularly after a major life or income change or when tax law changes. Events that may affect withholding include starting or leaving a job, working multiple jobs, marriage, divorce, the birth or adoption of a child, or a significant change in income.

The IRS Tax Withholding Estimator can help workers determine whether they are having too much or too little federal income tax withheld. The free online tool uses information such as recent pay statements, income, deductions, and credits to estimate federal income tax withholding. 

If an adjustment is needed, workers can use the estimator results to help complete a new Form W-4 and submit it to their employer. Form W-4 should not be sent to the IRS.

Employers and payroll professionals: Keep payroll taxes on track and protected

Employers and payroll professionals play an important role in the nation’s tax system by withholding, reporting, and depositing employment taxes.

The IRS encourages employers to regularly review their payroll processes and use current IRS guidance. Key responsibilities include:

  • Withhold employment tax accurately: Employers generally must withhold federal income tax, Social Security tax, and Medicare tax from employees’ wages.
  • Deposit federal taxes electronically: Federal tax deposits must be made by electronic funds transfer. Available options include the Electronic Federal Tax Payment System (EFTPS), IRS Direct Pay for businesses, and Business Tax Account for eligible users.
  • File employment tax returns on time: Employers can electronically file many employment tax records, including Forms 940, 941, 943, 944, and 945.
  • Maintain payroll records: Employers should keep all records of employment for at least four years.
  • Protect payroll data: Employers and payroll professionals should verify changes to direct deposit or employee information through a trusted channel, limit access to payroll systems, use multifactor authentication, and remain alert to phishing and credential theft. 

Publication 15, (Circular E), Employer’s Tax Guide provides information employers need to meet their federal employment tax responsibilities. Publication 15-T, Federal Income Tax Withholding Methods provides federal income tax withholding methods and tables.

Webinar for the payroll community

Payroll professionals can register for the free Sept 8 webinar, IRS and Payroll Professionals – Partners in Every Paycheck, for updates on federal employment tax deposits, Trump Account employer contributions, 2026 Form W-2 reporting changes, and IRS payroll resources. 

IRS resources for the payroll community

The IRS provides resources throughout the year for employers and payroll professionals, including:

  • Payroll Professionals Tax Center
  • Understanding Employment Taxes
  • Tax Withholding Estimator
  • Publication 15, (Circular E), Employer’s Tax Guide
  • Publication 15-T, Federal Income Tax Withholding Methods
  • Business Tax Account
  • E-file Employment Tax Forms

Payroll professionals can also subscribe to taxassistant for Payroll Professionals for updates about federal payroll reporting, employment tax procedures, IRS announcements, and other developments affecting payroll tax returns.

1. Why does the IRS recommend that workers review their tax withholding before or during National Payroll Week?

Major life changes (like getting married, having a child, starting a second job, or changing income levels) alter your overall tax liability. Checking your tax withholding helps ensure your employer takes out the correct amount of federal income tax from each paycheck, preventing a surprisingly large tax bill or underpayment penalties when you file your tax return.

2. How do employees adjust their federal tax withholding, and do they submit Form W-4 to the IRS?

Employees can use the free IRS Tax Withholding Estimator tool online to determine if they need to adjust their tax withholding. If an adjustment is necessary, the tool helps complete a new Form W-4 (Employee’s Withholding Certificate). Employees must submit this new Form W-4 directly to their employer—it should not be sent to the IRS.

3. What specific taxes are employers required to withhold from employee paychecks?

Employers are required to accurately withhold Federal Income Tax, Social Security tax, and Medicare tax (collectively referred to as employment or payroll taxes) from their employees’ wages.

4. How are employers required to deposit federal employment taxes, and what platforms can they use?

Employers must deposit federal employment taxes electronically. Acceptable IRS electronic payment channels include: EFTPS (Electronic Federal Tax Payment System) IRS Direct Pay for Businesses Business Tax Account

5. How long must employers keep payroll and employment tax records?

Employers are required to maintain all employment tax records for at least 4 years.