Payroll Software Compatible with Xero: What to Look for and Why It Matters

June 18, 2025
Payroll Software Compatible with Xero

If you’re already using Xero to manage your business accounts, integrating payroll software that’s compatible with Xero can save you hours of manual data entry, reduce errors, and give you real-time financial insights. But not all payroll systems are a good fit—and when you're in a complex industry like construction or contracting, especially under the Construction Industry Scheme (CIS), choosing the right software becomes even more critical.

In this article, we’ll explore the benefits of using payroll software that integrates with Xero and what features you should look for to ensure a smooth and efficient payroll process.


Why Xero-Compatible Payroll Software is a Game Changer

Xero has become the go-to cloud accounting software for small businesses, thanks to its intuitive interface, real-time reporting, and wide range of integrations. But when it comes to payroll, particularly for contractors or recruitment agencies, built-in solutions can fall short.

By choosing payroll software that syncs directly with Xero, you can:

  • Eliminate duplicate data entry
    No more copy-pasting figures or manually importing CSV files. Payroll journals, PAYE liabilities, and CIS deductions can all be automatically pushed into Xero.
  • Improve compliance
    Good payroll software should handle Real Time Information (RTI) submissions, student loans, holiday pay, and CIS deductions.
  • Improve cash flow visibility
    Accurate and timely posting of payroll data into Xero means you can instantly see your cash position and liabilities without waiting for month-end reconciliations.
  • Reduce admin time
    Save hours each week by automating repetitive tasks like payslip generation, FPS submissions, and pension reporting.

Key Features to Look for in Xero-Compatible Payroll Software

Not every Xero-compatible payroll app is the right fit—especially if you’re managing CIS contractors or running weekly payroll. Here are some features that matter:

1. Real-Time Xero Journal Syncing

Choose software that posts journals into Xero the moment a pay run is approved. This avoids timing errors and helps keep your books current.

2. Support for CIS Deductions

If you're in construction, make sure your payroll software can handle CIS gross, net, and deduction status—and automatically reflect this in both payroll and Xero journal entries.

3. Customisable Chart of Accounts Mapping

Look for payroll software that lets you map wage types, tax, pensions, and CIS deductions to specific Xero accounts. This allows greater control over reporting and reconciliation.

4. Automatic Invoice Creation for Umbrella or Agency Models

If you run an umbrella company or a recruitment agency, the ability to auto-generate invoices for client companies and sync them to Xero can be a massive time-saver.

5. Pension and RTI Automation

Software should support NEST, The People's Pension, and other major pension providers. It should also handle RTI submissions automatically, including FPS and EPS.


Final Thoughts

Choosing payroll software that’s compatible with Xero is a necessity for businesses that want to streamline their operations, reduce costs, and stay compliant. If you’re a contractor, accountant, or agency working under tight margins and stricter regulations, investing in the right software setup could make all the difference.


Need help finding the right payroll software that works with Xero?
We offer a professional Xero Software Development and Integration service. Please get in touch to learn more.

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