How to Conduct Payroll Audit with Checklist?

Payroll Audit Checklist & Internal Control
Kristen Larson
By Kristen Larson
April 17, 2024
7 mins read

Conducting a payroll audit is crucial for businesses of all sizes to ensure the accuracy and compliance of their payroll systems with various tax and employment laws. Such audits are not just a matter of financial hygiene; they are essential in detecting discrepancies, preventing potential fraud, and upholding the integrity of financial records. They play a significant role in verifying that employees are compensated fairly and by legal standards. 

An effective payroll audit scrutinizes every aspect of the payroll process, from employee classification and hours worked to tax withholdings and record-keeping. 

This article provides an insightful and detailed guide on performing a thorough payroll audit. It includes a comprehensive payroll audit checklist designed to streamline the control process, making it more efficient and effective for businesses aiming to maintain robust and compliant payroll practices.

payroll audit checklist

The Importance of Payroll Audits

Payroll audits are integral to the financial health and legal compliance of a business. By thoroughly examining your company's payroll processes, these audits ensure that employees are paid the correct amounts and that proper deductions are made consistently. This task is not just about checking numbers; it's about upholding fairness, accuracy, and legal compliance in compensation. 

Payroll audits help in identifying any inadvertent errors or intentional misrepresentations that could lead to significant financial and legal repercussions. They also verify that the company's policies for payroll internal controls align with ever-evolving tax laws and employment regulations. 

By conducting regular payroll audits, businesses can protect themselves from costly penalties, maintain trust with their employees, and demonstrate a commitment to ethical business practices. These audits serve as a critical tool in managing and safeguarding a company's financial integrity and reputation in the marketplace.

Beginning Your Payroll Audit with 8 Steps

Conducting a payroll audit is a meticulous process that requires a systematic approach. This section elaborates on the key steps to ensure a thorough and effective audit.

1. Gather Necessary Documents

Begin by assembling all relevant payroll stub records. This comprehensive collection should include timesheets, pay stubs, tax forms, and employee records. It's essential to have a complete set of documents as they form the basis of your audit. Ensure you have records from multiple periods to check for consistency and accuracy over time.

2. Review Employee Information

Accurately maintaining employee information is crucial. Check each employee's personal details, such as their name, social security number, address, and job title. Mistakes in this data can lead to serious issues like incorrect tax filings or benefits allocations. Regularly updating and verifying these details is key to maintaining an accurate payroll system.

3. Verify Time and Attendance Records

The next step is to ensure the hours worked, as recorded in timesheets, align with those paid in the payroll system. This verification process is vital to prevent overpayments or underpayments. Pay special attention to overtime calculations and ensure they comply with legal standards. Discrepancies here often signal errors in payroll processing or timekeeping.

4. Inspect Pay Rates and Payroll Changes

Confirm that each employee is paid according to their agreed-upon rate. Any changes in pay, such as raises or bonuses, should be documented and reflected accurately in the payroll. This step involves cross-referencing human resources records and payroll data to ensure every adjustment is authorized and correctly implemented.

5. Analyze Payroll Taxes and Deductions

Carefully scrutinize the calculation and remittance of payroll taxes. It's crucial to comply with federal, state, and local tax laws to avoid penalties. Ensure deductions for health insurance, retirement contributions, and other benefits are accurate and in line with employee selections. This step often involves a detailed review of payroll software settings and tax tables.

6. Check Payroll Classification

Misclassifying employees can lead to legal and financial complications. Ensure each worker is correctly classified as either exempt or non-exempt for overtime purposes. This classification affects how employees are paid for overtime and can impact compliance with labor laws.

7. Audit Leave and Benefits

Review the administration of paid time off, sick leave, and other benefits. Verify that employees are accruing and using their leave according to policy. Ensure that leave balances are accurately recorded and reflected in the payroll. This step is crucial for maintaining employee morale and trust.

8. Evaluate Payroll System Security

Finally, assess the security measures in place to protect sensitive payroll check stub data from unauthorized access. This includes physical security (for paper records) and cyber security (for electronic data). Ensure that access to payroll information is restricted to authorized personnel and that there are strong protocols for data protection and privacy.

Need to Know: Payroll Reports Types and Examples

Detailed Payroll Audit Checklist

A meticulous payroll audit is crucial for any organization to ensure accuracy, compliance, and efficiency in its payroll system. Below is a detailed checklist that can guide you through the process:

Employee Data Verification

Accuracy of Personal Information: Rigorously confirm the correctness of each employee's personal details, including name, address, social security number, and contact information. Inaccuracies here can lead to serious tax and communication issues.

Classification Check: Carefully review the classification of each employee as full-time, part-time, or contractor. Misclassification can result in legal issues and incorrect payroll processing.

Pay Rate Assessment

Contract Alignment: Verify that the pay rates for each employee align with their employment contracts or agreements. This step is crucial to ensure that employees are compensated as per their agreed terms.

Salary Adjustments and Bonuses: Review any changes to employee pay, including raises, bonuses, or other adjustments. Ensure these changes are authorized, documented, and accurately reflected in the payroll.

Timesheet and Attendance Analysis

Matching Records: Match time records with payroll data to ensure that employees are paid for the actual hours worked. This includes verifying regular hours, overtime, and any other time categories.

Discrepancy Investigation: Investigate any differences between the hours worked (as per timesheets) and hours paid. This helps in identifying errors or potential fraud.

Tax Deductions and Contributions Review

Federal and State Taxes: Ensure that the calculation and payment of federal and state taxes are accurate and comply with current tax laws. This includes validating tax rates and ensuring proper withholdings.

Nice to Know: FUTA and SUTA Taxes

Social Security and Medicare Contributions: Verify correct deductions for social security and Medicare. This also involves checking employer contributions to ensure compliance with FICA regulations.

Benefits and Leave Scrutiny

Accuracy of Paid Time Off: Check the accuracy of vacation, sick leave, and other paid time off records. Ensure that employees' leave balances are correct and that leave policies are consistently applied.

Benefits Enrollment and Deductions: Review the enrollment in employee benefits such as health insurance, retirement plans, and any associated deductions from payroll. This ensures that benefits are properly administered and deducted.

Compliance with Employment Laws

Minimum Wage Compliance: Confirm that all employees are paid at least the minimum wage as per federal, state, and local laws. This is fundamental to avoid legal penalties.

Overtime Regulations: Ensure compliance with overtime pay regulations. This includes verifying that non-exempt employees are correctly compensated for overtime hours.

Payroll System Security Check

Data Security Measures: Assess the robustness of measures in place to protect payroll data against unauthorized access, breaches, or other cybersecurity threats.

Access Controls: Review the controls governing access to sensitive payroll information. Ensure that access is restricted to authorized personnel and that there are protocols for secure data handling.


What is a payroll audit?

A payroll audit is a thorough review of a company's payroll processes to ensure accuracy in employee payments and compliance with tax and employment laws. It involves verifying the correctness of employee data, pay rates, deductions, tax withholdings, and adherence to relevant labor regulations.

Why is a payroll audit important?

Payroll audits are important to identify and correct discrepancies in payroll, prevent potential fraud, and ensure compliance with legal requirements. They also help maintain accurate financial records and foster trust among employees by ensuring fair and consistent pay practices.

Who should conduct a payroll audit?

Payroll audits can be conducted by internal audit teams or external auditors. Internal audits are beneficial for regular checks, while external auditors provide an unbiased perspective and specialized expertise, particularly for comprehensive annual audits.

What documents are needed for a payroll audit?

Essential documents for a payroll audit include timesheets, pay stubs, employee records, tax forms, and records of payroll changes such as raises or bonuses. Accurate and comprehensive documentation is key to an effective audit.

How often should a payroll audit be conducted?

The frequency of payroll audits depends on the size and complexity of the business. Generally, it's advisable to conduct a full payroll audit annually, with smaller, more focused audits occurring quarterly or semi-annually.

What are common findings in payroll audits?

Common findings include misclassification of employees, errors in pay rates or hours worked, incorrect tax withholdings, and discrepancies in benefit deductions. Identifying these issues allows for timely corrections and improvements in payroll processes.

How can a business prepare for a payroll audit?

Businesses can prepare for a payroll audit by maintaining organized and up-to-date payroll records, ensuring compliance with current tax laws and employment regulations, and regularly reviewing payroll processes for any discrepancies or changes.

What are the consequences of not conducting payroll audits?

Neglecting payroll audits can lead to significant legal and financial risks, including penalties for non-compliance with tax and labor laws, financial losses due to errors or fraud, and damage to employee morale and trust due to payroll inaccuracies.

What payroll is included in a workers' compensation audit?

In a workers' compensation audit, payroll includes all employee earnings such as salaries, wages, bonuses, commissions, and overtime pay.

Final Thoughts

A comprehensive payroll audit is more than a compliance exercise; it's a critical component of a company's financial and operational integrity. Regularly conducting a detailed payroll audit as outlined in this checklist can help businesses identify and rectify errors, prevent fraud, and ensure adherence to various regulatory requirements. 

By maintaining an accurate and compliant payroll system, organizations not only safeguard themselves against legal and financial pitfalls but also foster trust and transparency with their employees.

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