Setting up payroll in QuickBooks Desktop is a crucial task for businesses to ensure employees are paid accurately and on time. This detailed guide will walk you through the steps to easily set up payroll in QuickBooks Desktop, helping you streamline your payroll process and maintain compliance with tax regulations.

Step 1: Choose a QuickBooks Desktop Payroll Service

QuickBooks Desktop offers different payroll services to cater to various business needs. The main options include:

  1. Basic Payroll: Calculates payroll taxes and allows you to create paychecks.
  2. Enhanced Payroll: Includes tax forms and e-filing capabilities, along with the features of Basic Payroll.
  3. Assisted Payroll: A full-service option where Intuit handles your payroll taxes and filings.

Evaluate your business requirements and select the payroll service that best suits your needs. Once you’ve chosen a service, you’ll need to activate it within QuickBooks Desktop.

Step 2: Set Up Payroll Preferences

  1. Open Payroll Setup: In QuickBooks Desktop, go to the "Employees" menu and select "Payroll Setup."
  2. Enter Company Information: Provide essential details about your business, such as the legal name, address, and Employer Identification Number (EIN).
  3. Payroll Preferences: Configure your payroll preferences, including pay schedules, employee benefits, and deductions. This setup ensures that QuickBooks can accurately calculate payroll and deductions.

Step 3: Enter Employee Information

Accurate employee information is vital for correct payroll processing. Here’s how to add your employees:

  1. Go to Employee Center: Navigate to the "Employees" menu and select "Employee Center."
  2. Add New Employee: Click “New Employee” and fill in the required details, including name, address, Social Security Number (SSN), and contact information.
  3. Set Up Compensation Details: Specify each employee’s pay rate (hourly or salary), overtime rate, bonuses, and commissions if applicable.
  4. Enter Tax Information: Include federal and state tax withholdings based on the employee’s W-4 form. QuickBooks will use this information to calculate the appropriate tax deductions.

Step 4: Configure Payroll Items

Payroll items represent the various types of earnings and deductions for employees. Setting them up correctly ensures accurate payroll calculations.

  1. Create Payroll Items: Navigate to the "Lists" menu and select "Payroll Item List." Click "Payroll Item" and choose "New" to create a new payroll item.
  2. Add Earnings Items: Create items for regular pay, overtime, bonuses, and commissions. QuickBooks provides guided steps to help you set up each item.
  3. Set Up Deductions: Include deductions for taxes, health insurance, retirement plans, garnishments, and other withholdings. Each deduction item must be set up with the correct tax tracking type.

Step 5: Set Up Payroll Schedules

Setting up payroll schedules ensures that your employees are paid consistently and on time.

  1. Navigate to Pay Schedules: From the "Employees" menu, select "Payroll Setup" and then "Pay Schedules."
  2. Create Pay Schedule: Click "Create pay schedule" and choose the frequency that matches your payroll cycle (weekly, bi-weekly, semi-monthly, or monthly).
  3. Assign Employees to Pay Schedules: Assign each employee to the appropriate pay schedule. This will automate the payroll process based on the frequency you selected.

Step 6: Configure Payroll Taxes

Properly configuring payroll taxes is crucial for compliance with tax regulations.

  1. Access Payroll Tax Setup: In the Payroll Setup window, go to the "Taxes" section.
  2. Enter Federal Tax Details: Provide your EIN, tax filing frequency, and deposit schedule. QuickBooks will guide you through entering this information to ensure compliance.
  3. State and Local Taxes: Enter state tax information, including state EIN, tax rates, and any additional state-specific requirements. If applicable, configure local tax rates and details.

Step 7: Set Up Direct Deposit

Direct deposit is a convenient way to pay employees. To set it up:

  1. Enroll in Direct Deposit: Go to the "Employees" menu, select "My Payroll Service," and then "Activate Direct Deposit."
  2. Enter Bank Information: Provide your business’s bank account details for payroll funds.
  3. Verify Bank Account: QuickBooks will initiate small test deposits to verify the bank account. Confirm these amounts to complete the verification process.
  4. Add Employee Bank Details: Enter each employee’s bank account information for direct deposit. Ensure that the information is accurate to avoid payment issues.

Step 8: Run Your First Payroll

With everything set up, you’re ready to run your first payroll.

  1. Go to the Employees Menu: Select “Pay Employees” and then “Scheduled Payroll.”
  2. Select Pay Schedule: Choose the pay schedule you’ve set up for your employees.
  3. Review Employee Hours and Earnings: Enter the hours worked for hourly employees and verify salary amounts for salaried employees. Ensure all data is accurate before proceeding.
  4. Preview Payroll: Review the payroll summary, ensuring all details are correct. This includes verifying pay rates, deductions, and tax withholdings.
  5. Create Paychecks: Click “Create Paychecks” to process the payroll. QuickBooks will handle calculations and direct deposits.
  6. Print or Distribute Pay Stubs: Print paychecks or distribute electronic pay stubs to employees. Ensure that all employees receive their payment details.

Step 9: File Payroll Taxes

QuickBooks simplifies tax filing and payments. Here’s how to stay compliant:

  1. Access Payroll Tax Center: Go to the "Employees" menu, select "Payroll Taxes and Liabilities," and then "Pay Scheduled Liabilities."
  2. Review Tax Forms: QuickBooks generates the necessary federal and state tax forms based on your payroll data.
  3. Submit Tax Payments: Follow the prompts to submit your payroll tax payments electronically. Ensure payments are made on time to avoid penalties.
  4. File Tax Forms: Ensure timely filing of all required tax forms, such as Form 941, Form 940, and state-specific forms. QuickBooks provides reminders and guidance for filing these forms.

Step 10: Generate Payroll Reports

Payroll reports provide valuable insights into your payroll expenses and help with compliance. To generate reports:

  1. Go to the Reports Menu: Select "Employees & Payroll" to access payroll reports.
  2. Choose Report Type: Generate reports such as Payroll Summary, Payroll Detail, Tax Liability, and Employee Earnings. These reports provide a comprehensive view of your payroll data.
  3. Customize and Export: Customize report parameters as needed and export reports for record-keeping or further analysis. Regularly reviewing these reports helps ensure accurate payroll management and compliance with regulations.


Set up payroll in QuickBooks Desktop can be straightforward and efficient when following these steps. By choosing the right payroll service, entering accurate company and employee information, setting up pay schedules, configuring payroll taxes, and running payroll correctly, you can ensure smooth and compliant payroll operations. QuickBooks Desktop not only simplifies payroll management but also helps you stay compliant with tax regulations, allowing you to focus on other important aspects of your business. Start your payroll setup today and experience the benefits of streamlined payroll processes with QuickBooks Desktop.