How To Run Manual Payroll : Step-by-Step Guide for Small Businesses

Running payroll is an essential task for any business, ensuring employees are compensated accurately and on time. While many businesses opt for automated payroll systems, some small businesses prefer to handle payroll manually due to various reasons such as budget constraints or the need for greater control over the process. In this comprehensive guide, we will walk you through the steps of manual payroll processing and discuss the pros and cons of this approach.

A Step-by-Step Guide: How To Run Payroll Manually

Running payroll manually involves several key steps to ensure accuracy and compliance with tax regulations. Let’s break down the process into manageable steps:

Why Choose Manual Payroll?


  • Cost-Effective: Manual payroll systems are generally more affordable, making them accessible for small businesses with limited budgets.
  • Greater Control: Businesses have complete control over the payroll process, allowing for customization and flexibility.
  • Enhanced Understanding: Managing payroll manually provides a deep understanding of the company’s financials and employee compensation structure.
  • No Dependence on Technology: Manual systems eliminate the risk of technical glitches or software failures disrupting payroll operations.


  • Time-Consuming: Manual payroll processing can be time-consuming, especially for businesses with numerous employees.
  • Error-Prone: Human errors are more likely to occur during manual calculations, leading to potential payroll discrepancies.
  • Compliance Challenges: Keeping up with changing tax laws and regulations can be challenging without automated assistance.
  • Limited Scalability: Manual systems may become inefficient as the business grows and the number of employees increases.

Step #1: Getting Started With Payroll

Before diving into the payroll process, ensure you have all the necessary documents and information, including employee records, tax forms, and compensation details.

Step #2: Employee Onboarding and Payroll

  • Collect Tax Information: Gather W-4 forms from employees to determine withholding tax.
  • Classify Employees: Determine the classification of employees (full-time, part-time, contractor) for accurate payment calculations.
  • Set Up Compensation: Establish clear guidelines for hourly wages, salaries, bonuses, and other forms of compensation.

Step #3: Understanding Payroll Taxes

Federal Payroll Taxes

Understanding federal payroll taxes is crucial for compliance. These taxes include income tax withholding, Social Security tax, and Medicare tax.

State and Local Taxes

In addition to federal taxes, businesses must comply with state and local tax regulations, which vary by location. Research the specific requirements for your business’s location to ensure compliance.

Step #4: Calculate Payroll

Step #1: Gather Data

Collect employee work hours, overtime, bonuses, and any other relevant data.

Step #2: Calculate Gross Pay

Calculate gross pay based on the agreed-upon compensation structure.

Step #3: Deduct Taxes

Deduct federal, state, and local taxes as per the employee’s tax withholding information.

Step #4: Make Any Other Deductions

Consider other deductions such as retirement contributions, health insurance premiums, or garnishments.

Step #5: Determine Net Pay

Calculate the net pay by subtracting all deductions from the gross pay.

Step #6: Distribute Payment

Process payments via checks or direct deposit and provide employees with detailed pay stubs.

Step #5: Keep Records and Reports

Maintain accurate records of payroll calculations, tax withholdings, and payments. Regularly generate reports to track payroll expenses and ensure compliance with tax authorities.

How To Run Payroll Manually: Is It the Best Way?


  • Cost-Effective Solution: Especially beneficial for small businesses with limited budgets.
  • Enhanced Control: Allows businesses to have complete control over payroll operations.
  • Better Understanding: Provides a deep understanding of payroll intricacies and financial aspects of the business.


  • Time-Consuming: Manual payroll processing can be time-intensive, taking away valuable time from other business activities.
  • Increased Error Risk: Human errors in calculations can lead to payroll discrepancies and legal issues.
  • Compliance Challenges: Keeping up with changing tax laws without automated assistance can be daunting.

In conclusion, while manual payroll processing offers cost-effectiveness and control, it requires meticulous attention to detail and ongoing effort to stay compliant with tax regulations. For small businesses with a limited number of employees and a keen eye for detail, manual payroll can be a viable option. However, as businesses grow, transitioning to automated payroll systems might become a necessary step to ensure efficiency, accuracy, and compliance.