Fix Xero Payroll Sync Error - Employee Data Not Syncing

12-minute fixVerified for Xero Payroll 2025Medium difficulty

Quick Answer:

Xero payroll sync errors occur when employee data fails to sync between Xero and third-party systems like Deputy, Tanda, or Employment Hero. Common causes include missing payroll calendars, name/email mismatches, duplicate profiles, and unallocated pay items.

What is a Xero Payroll Sync Error?

Payroll sync errors prevent timesheet data, employee information, or pay run details from transferring correctly between Xero Payroll and integrated workforce management systems. This disrupts payroll processing and can cause payment delays.

Error Payroll Sync Error: Employee data not syncing with Xero Payroll

Integration failing to export timesheets or update employee information in Xero.

Symptoms:
  • •Employee profiles not appearing in Xero from integrated app
  • •"Pay details cannot be synced" error messages
  • •Timesheet export failing with validation errors
  • •Invalid Payroll Calendar ID errors
  • •Duplicate or inactive employee profile conflicts
  • •Leave requests preventing calendar sync
  • •Pay items missing or not allocated to expense accounts
Resolution Steps:
  1. 1.
    Verify payroll calendar is assigned to employees
  2. 2.
    Check name and email address exact matches
  3. 3.
    Remove duplicate employee profiles
  4. 4.
    Allocate pay items to correct expense accounts
  5. 5.
    Process unprocessed leave requests
  6. 6.
    Re-authorize integration connection

Quick Fix for Payroll Sync Error (12 Minutes)

Fastest Solution

  1. In Xero: Go to Payroll → Employees → Select employee
  2. Click Employment → Pay Calendar
  3. Ensure payroll calendar is assigned
  4. Verify employee Start Date, Email, and Name spelling matches integration exactly
  5. Check for duplicate profiles in inactive employees list
  6. Retry sync from integration app

Detailed Solution Steps

  • 1
    Verify Payroll Calendar Assignment

    Most common cause - missing or invalid payroll calendar:

    1. Log into Xero Payroll
    2. Navigate to Payroll → Employees
    3. Select the employee with sync issues
    4. Click on "Employment" tab
    5. Check "Pay Calendar" field
    6. If blank, select appropriate payroll calendar from dropdown
    7. Save changes and retry sync

    Error "Invalid Payroll Calendar ID" means the calendar ID from your integration doesn't match any calendar in Xero. Ensure calendar exists and is active.

  • 2
    Match Employee Name and Email Exactly

    Even minor differences prevent sync:

    Common Mismatches
    WRONG:                  CORRECT:
    John smith    vs    John Smith    (capitalization)
    JohnSmith     vs    John Smith    (spacing)
    john@co.com   vs    john@company.com (domain)
    John  Smith   vs    John Smith    (extra space)
     
    All fields must match EXACTLY:
    ✓ First Name
    ✓ Last Name
    ✓ Email Address
    ✓ Start Date
    1. Compare employee details in integration app vs Xero
    2. Check for extra spaces, different capitalization
    3. Update to match exactly (use copy/paste to ensure accuracy)
    4. Verify email is same including domain
    5. Save and retry sync
  • 3
    Remove Duplicate Employee Profiles

    Duplicates in inactive list cause sync failures:

    1. In Xero Payroll → Employees
    2. Click "Show inactive employees"
    3. Look for duplicate employee profiles
    4. If duplicate exists, reactivate the inactive profile
    5. Delete or merge the newer duplicate profile
    6. Ensure only one profile exists for each employee
    7. Retry integration sync

    This is the most common cause of persistent sync issues. Having both active and inactive profiles for the same person confuses the integration.

  • 4
    Allocate Pay Items to Expense Accounts

    Pay items must be properly configured:

    1. Go to Payroll → Settings → Pay Items
    2. Click on each Earnings Line/Pay Item type
    3. Ensure "Expense Account" field is populated
    4. Select appropriate expense account (e.g., Wages, Salaries)
    5. Save each pay item
    6. Return to integration and retry export
  • 5
    Process Unprocessed Leave Requests

    Pending leave can block entire employee sync:

    1. Check for error: "Payroll calendar cannot be changed due to unprocessed leave request"
    2. Go to Payroll → Leave
    3. Find pending/unprocessed leave requests for affected employee
    4. Either approve or decline the leave request
    5. Process the leave in next Xero pay run if approved
    6. Once processed, retry integration sync
  • 6
    Check API Rate Limits

    Xero has daily API limits that can cause sync failures:

    1. Xero limits to 5,000 API requests per calendar day
    2. If error mentions rate limit or quota exceeded
    3. Wait until next calendar day (usually resets at midnight UTC)
    4. Retry integration sync the following day
    5. If persistent, contact integration support to optimize API calls

    • Why Do Payroll Sync Errors Occur?

    Common Causes

    • Missing Payroll Calendar: Employee doesn't have a pay calendar assigned in Xero payroll settings
    • Data Mismatch: Employee name, email, or start date differs between integration and Xero
    • Duplicate Profiles: Inactive duplicate employee profile exists causing ID conflicts
    • Unallocated Pay Items: Pay items/earnings rates not assigned to expense accounts
    • Pending Leave Requests: Unprocessed leave blocking employee file updates
    • API Limits: Exceeded daily API request quota (5,000 per day)
    • Integration Connection Issues: Authorization expired or connection broken between apps

    How to Prevent Payroll Sync Errors

    Best Practices:

    • Always assign payroll calendar when creating new employees in Xero
    • Use copy/paste to ensure name and email fields match exactly across systems
    • Delete or properly archive inactive employees instead of leaving duplicates
    • Configure all pay items with expense accounts before first use
    • Process leave requests promptly to avoid blocking syncs
    • Test sync after adding new employees before payroll deadline

    Frequently Asked Questions

    Which integration apps does this apply to?

    These solutions work for most Xero Payroll integrations including Deputy, Tanda, Employment Hero, Workforce.com, Planday, and similar time tracking/payroll systems. The specific error messages may vary slightly but root causes are similar.

    What if only one employee won't sync?

    Single employee sync failures are usually due to that specific employee's profile having a data mismatch, missing calendar, or duplicate profile. Focus troubleshooting on that employee's Xero settings compared to the integration app.

    Can I manually enter timesheets if sync fails?

    Yes, as a temporary workaround you can manually enter pay run information in Xero Payroll while troubleshooting the integration sync. However, this defeats the purpose of the integration, so fix the root cause for long-term efficiency.

    How long does it take for sync fixes to take effect?

    Most fixes are immediate. After making changes in Xero (calendar assignment, name correction, etc.), you can retry the sync from your integration app right away. If still failing, wait 5-10 minutes and try again for any caching to clear.

    Related Resources

    Xero Integration Sync Failure

    Fix general app integration issues

    Xero Data Mapping Error

    Fix incorrect account assignments

    Need Professional Help?

    If payroll sync errors are affecting your pay runs and you need immediate resolution, our Xero payroll experts can diagnose integration issues and ensure smooth data flow between your systems.

    Get Expert Support