Xero Integration Sync Errors: E-commerce & Marketplace

12-minute fixVerified for Xero 2025Medium difficulty

Quick Answer:

Xero integration sync errors with Shopify, Amazon, eBay, and other platforms occur due to API authentication failures, broken connections, incorrect account mapping, or rate limiting. Fix by reconnecting apps, updating account mappings, and verifying API permissions.

What are Xero Integration Sync Errors?

Xero integration sync errors occur when third-party e-commerce platforms (Shopify, Amazon, eBay, Etsy, WooCommerce) or marketplace apps fail to transfer sales data, inventory levels, or order information to Xero. These errors prevent automatic financial data synchronization, requiring manual entry and causing reporting delays.

Error Integration Sync: Failed to sync data with Xero - Connection or mapping error

E-commerce or marketplace integration cannot sync transactions, orders, or inventory to Xero due to authentication, API, or mapping issues.

Symptoms:
  • Missing sales data in Xero from online stores
  • Integration app shows sync failed errors
  • Incorrect inventory levels between platforms
  • Failed order imports or duplicate transactions
  • Authentication expired or connection lost messages
Resolution Steps:
  1. 1.
    Reconnect integration app to Xero
  2. 2.
    Update account code mappings
  3. 3.
    Verify API permissions and scopes
  4. 4.
    Check for rate limit issues
  5. 5.
    Review and fix data mapping errors

Quick Fix for Sync Errors (12 Minutes)

Fastest Solution

  1. Log into your integration app (Link My Books, Webgility, A2X, etc.)
  2. Go to Settings or Connections
  3. Click "Disconnect" from Xero
  4. Wait 30 seconds
  5. Click "Connect to Xero"
  6. Log in to Xero and authorize the app
  7. Grant all requested permissions
  8. Return to integration app and verify connection
  9. Trigger manual sync to test
  10. If error persists, proceed to detailed steps

Detailed Solution Steps

  • 1
    Reconnect Integration to Xero

    Re-establish authentication between your integration app and Xero:

    1. Log into your integration platform (Shopify app, Amazon connector, etc.)
    2. Navigate to Settings → Integrations or Connections
    3. Find Xero connection status
    4. Click "Disconnect" or "Revoke Access"
    5. Confirm disconnection
    6. Wait 30-60 seconds for complete disconnect
    7. Click "Connect to Xero" or "Authorize Xero"
    8. You'll be redirected to Xero login page
    9. Log in with your Xero credentials
    10. Select the correct Xero organization
    11. Review requested permissions carefully
    12. Click "Allow access" to grant permissions
    13. Verify successful connection in integration dashboard

    Why Reconnect Works

    Reconnecting refreshes the API authentication token and re-establishes the secure connection between platforms. This fixes most authentication and permission-related sync errors.
  • 2
    Update Account Code Mappings

    Ensure transactions are mapped to active Xero accounts:

    1. In your integration app, go to Settings → Account Mapping
    2. Review all mapped Xero accounts:
    3. Sales/Revenue account
    4. Cost of Goods Sold (COGS)
    5. Shipping/Freight account
    6. Refunds account
    7. Fees/Expenses account
    8. Payment gateway account
    9. For each mapping, verify account still exists in Xero
    10. Log into Xero → Accounting → Chart of Accounts
    11. Ensure mapped accounts are not archived or deleted
    12. If account missing, update mapping to correct active account
    13. Click "Update Chart of Accounts" in integration app
    14. Save all mapping changes
    15. Test sync with a recent transaction

    Common Mapping Errors:

    Mapped to archived account → Update to active account
    Wrong tax code assigned → Fix in mapping settings
    Missing COGS mapping → Add product cost mapping
  • 3
    Verify Xero API Permissions

    Ensure integration has required access to Xero data:

    1. Log into Xero
    2. Go to Settings → Connected Apps
    3. Find your integration app in the list
    4. Click on the app name to view details
    5. Review granted permissions - should include:
    6. Read and write invoices
    7. Read and write contacts
    8. Read and write bank transactions
    9. Read chart of accounts
    10. Read and write items/inventory
    11. If permissions are insufficient, disconnect and reconnect app
    12. Grant all requested permissions during reconnection
    13. Test sync after permissions update
  • 4
    Check for API Rate Limiting

    Xero API has rate limits that can cause sync failures:

    1. Check integration app for rate limit warnings
    2. Xero rate limits (per organization):
    3. 60 API calls per minute
    4. 5,000 API calls per day
    5. 10,000 API calls per day for partner apps
    6. If hitting limits, adjust sync frequency:
    7. Change from real-time to hourly sync
    8. Reduce number of synced items
    9. Schedule syncs during off-peak hours
    10. Wait for rate limit reset (usually 1 hour)
    11. Retry sync after waiting period
    Xero API Rate Limits
    Per Minute: 60 calls
    Per Day: 5,000 calls (standard) / 10,000 (partner)
    Limit Reset: Hourly rolling window
    Error Response: 429 Too Many Requests
  • 5
    Review Integration Error Logs

    Identify specific sync errors from detailed logs:

    1. In integration app, find Error Logs or Sync History
    2. Look for recent failed syncs
    3. Click on failed transaction to view error details
    4. Common error messages and solutions:
    5. "Account code archived" → Update account mapping
    6. "Invalid tax code" → Fix tax rate mapping
    7. "Contact not found" → Create customer in Xero
    8. "Duplicate invoice" → Check for existing invoice
    9. "Authentication failed" → Reconnect to Xero
    10. Fix identified issues based on error message
    11. Use "Retry" button to resync failed transactions
    12. Monitor for successful sync completion
  • 6
    Fix Product and Tax Code Mapping

    Ensure products and tax rates sync correctly:

    1. In integration app, go to Product Mapping or SKU Mapping
    2. Review product assignments to Xero items
    3. For unmapped products:
    4. Create matching item in Xero inventory
    5. Or assign to existing Xero item code
    6. Check tax code assignments:
    7. Tax Exempt → Tax Exempt in Xero
    8. Standard Rate → Tax on Sales (20% UK, varies by country)
    9. Zero Rate → Zero Rated Expenses/Sales
    10. Save all product and tax mappings
    11. Run "Update Product Catalog" if available
    12. Test with a sample order containing mapped products
  • 7
    Clear Integration Cache and Retry

    Reset integration app data cache:

    1. In integration app settings, look for "Clear Cache" option
    2. Click "Clear Cache" or "Reset Sync"
    3. This removes temporary sync data and resets connection
    4. Log out of integration app
    5. Clear browser cache and cookies
    6. Log back into integration app
    7. Verify Xero connection is still active
    8. Trigger manual sync for failed transactions
    9. Monitor sync progress and check for errors
  • 8
    Contact Integration Support

    If errors persist, get help from integration provider:

    1. Gather error details before contacting support:
    2. Exact error messages
    3. Transaction IDs that failed
    4. Screenshots of error logs
    5. When error first occurred
    6. Contact integration app support via:
    7. In-app chat or support ticket
    8. Email support team
    9. Phone support (if available)
    10. Provide all gathered information
    11. Follow their specific troubleshooting steps
    12. Request escalation if standard fixes don't work

    Popular Integration Support

    Link My Books: support@linkmybooks.com
    A2X: support.a2xaccounting.com
    Webgility: support.webgility.com
    Amaka: help.amaka.io
  • Why Do Integration Sync Errors Occur?

    Root Causes

    • API Authentication Expiry: Xero API token expires after period of inactivity or when permissions are revoked
    • Account Mapping Errors: Transactions mapped to archived, deleted, or locked Xero accounts
    • API Changes: Xero or e-commerce platform updates API, breaking existing integration
    • Rate Limiting: Too many API calls in short period trigger Xero's rate limits
    • Missing Product Mappings: New products added to store without corresponding Xero item mapping
    • Tax Code Conflicts: Different tax rates or codes between platform and Xero causing sync rejection
    • Insufficient Permissions: Integration lacks required API scopes to read/write specific Xero data

    How to Prevent Integration Sync Errors

    Best Practices:

    • Monitor integration sync status daily and review error logs regularly
    • Map all products and account codes during initial setup before going live
    • Avoid archiving Xero accounts used in integration mappings without updating first
    • Keep integration apps updated to latest version to support API changes
    • Set up email notifications for sync failures to catch issues immediately

    Frequently Asked Questions

    Why did my Shopify-Xero integration stop working?

    Most commonly, the API authentication token expired or Xero account mappings changed. Try reconnecting the integration to refresh authentication, and verify that mapped accounts in Xero haven't been archived or deleted.

    Can I sync historical data after fixing the error?

    Yes, most integration apps have a "Resync" or "Retry Failed Transactions" feature. After fixing the error, you can manually trigger syncs for historical orders. Check your integration app's documentation for specific date range sync capabilities.

    Which integration app is best for my platform?

    For Shopify: Link My Books or Amaka. For Amazon: Link My Books or A2X. For multi-channel: Webgility or Link My Books. For eBay/Etsy: Link My Books. Choose based on your platform, transaction volume, and required features like inventory sync or multi-currency support.

    Will fixing the sync create duplicate transactions?

    Good integration apps prevent duplicates by checking for existing transactions before syncing. If you manually entered data during the sync failure, check for duplicates after fixing and delete any manual entries that are now synced automatically.

    Related Resources

    Need Professional Help?

    If you're still experiencing integration sync errors after following these steps, or need help with Xero e-commerce setup and account mapping, our Xero integration specialists are here to help.

    Get Expert Support