Xero Payroll Setup: A Complete Walkthrough

January 28, 2026 7 min read
Xero Payroll Setup: A Complete Walkthrough

Setting up payroll in Xero can significantly streamline your business operations, ensuring your employees are paid accurately and on time. In this comprehensive guide, we'll walk you through the entire process of setting up Xero Payroll, from initial setup to managing ongoing payroll tasks. By the end of this article, you'll have a clear understanding of how to efficiently manage payroll within Xero, helping to save time and reduce errors.

Why Choose Xero for Payroll?

Xero is a powerful cloud-based accounting software that provides a robust payroll feature. Here are some reasons why businesses opt for Xero Payroll:

  • Integration: Seamlessly integrates with your accounting data, providing a unified platform for managing finances.
  • Automation: Automates calculations and tax filings, reducing manual errors and saving time.
  • Compliance: Keeps you up-to-date with the latest tax and employment regulations.
  • Accessibility: Access your payroll data from anywhere, anytime, on any device.

Step-by-Step Guide to Setting Up Xero Payroll

Follow these steps to set up Xero Payroll efficiently:

1. Set Up Your Organisation Details

Before diving into payroll specifics, ensure your organisation's details are correctly set up:

  1. Log in to your Xero account.
  2. Navigate to Settings and select Organisation Settings.
  3. Fill in your business and contact details accurately.
  4. Ensure your financial settings are configured, including your default accounts for wages, superannuation, and PAYE.

2. Add Employees

Adding employees is a critical step in the setup process:

  1. Go to Payroll in the main menu and select Employees.
  2. Click on Add Employee.
  3. Enter each employee's personal, contact, and employment details. Ensure the information is accurate to prevent payroll discrepancies.
  4. Specify their tax codes, pay rates, and deductions if applicable.

3. Configure Payroll Settings

Next, configure the payroll settings to match your company’s requirements:

  1. Select Payroll Settings from the Payroll menu.
  2. Set up pay calendars, ensuring you choose the correct pay cycle (weekly, fortnightly, monthly).
  3. Define your statutory obligations, such as PAYE and National Insurance contributions.
  4. Set up direct deposit details for efficient salary disbursement.

4. Set Up Pay Templates

Pay templates allow you to standardise pay details for different roles:

  1. In the Payroll menu, select Employees and then click on the employee’s name.
  2. Navigate to the Pay Template tab.
  3. Add pay items such as base salary, allowances, and deductions.
  4. Ensure each pay item is linked to the correct account and tax setting.

5. Establish Leave Types and Policies

Ensure that your leave policies are clearly defined and set up in Xero:

  1. Go to Payroll Settings and select Leave.
  2. Define the leave types your organisation offers, such as annual leave, sick leave, and parental leave.
  3. Set accrual rates and balance limits as per your company policy.

Ongoing Payroll Management

Processing Payroll

Once setup is complete, processing payroll in Xero is straightforward:

  1. Navigate to Payroll and select Pay Runs.
  2. Click on New Pay Run and select the appropriate pay calendar.
  3. Review the pay run summary, ensuring all details are correct.
  4. Submit the pay run for approval and process payments to employees.

Reporting and Compliance

Xero provides a variety of reports to help you stay compliant and informed:

  • Use the Payroll Activity report to monitor employee pay and deductions.
  • Generate the PAYE Reconciliation report to ensure all taxes are correctly reported.
  • Review the Employee Leave report to manage leave balances and accruals.

Data Security and Backup with Boxkite

Handling payroll data responsibly is crucial for compliance and trust. Regular data backups ensure that your sensitive payroll information is safe from accidental loss or corruption. Boxkite offers an automated solution to back up your Xero accounting data, including payroll details, directly to your Dropbox account. This ensures that you have secure, easily accessible backups should you need to restore your data at any point.

Conclusion

Setting up Xero Payroll doesn't have to be a daunting task. By following this walkthrough, you'll be well on your way to efficiently managing your payroll processes, ensuring accuracy and compliance with minimal effort. Remember, safeguarding your data is just as important as processing it. With Boxkite, you can rest easy knowing your payroll data is securely backed up and protected.

Ready to take control of your payroll processes? Try Boxkite today and ensure your data is always secure and backed up.

Disclaimer: This article is intended for informational purposes only and does not constitute legal or tax advice. Please consult a professional for specific advice applicable to your circumstances.