Xero issues keep disrupting your accounting processes? Working with this popular cloud-based accounting software can lead to reconciliation and syncing problems that impact your business operations.
Xero serves as the backbone for many small businesses and accounting firms' daily financial management. However, many users face unexpected challenges with Xero, which we’re going to discuss in this article.
After reading this guide, you'll be able to identify these common Xero issues and find ways to fix them to maintain seamless financial operations.
Common Xero issues and ways to fix them
Here are some of the most common Xero issues, organized by category and automated solutions to ensure better financial visibility and operational agility:
1. Bank feed and reconciliation issues
1) Bank feeds not updating or missing transactions
Bank feeds may stop working due to changes in their security protocols, expired connections, or technical issues between Xero and the bank's systems.
How to fix it:
- Go to Bank Accounts > Manage Account > Update Feed
- Reconnect your bank feed if prompted
- Confirm credentials and permissions at the bank level
- Manually import transactions using CSV if syncing fails
- Contact Xero support if the issue persists beyond 48 hours
2) Duplicate transactions appearing
This happens when transactions are imported multiple times through different methods (bank feed + manual import or multiple feed connections).
How to fix it:
- Identify the source of duplicate transactions (manual import vs. bank feed vs. multiple connections)
- Delete only manually imported entries (never delete bank feed data)
- Check bank feed settings to prevent automatic future duplicates
- Use Xero's 'Find & Match' feature to merge legitimate duplicates
- Avoid importing data for periods already covered by feeds
3) Bank reconciliation won't balance
When the ending balance in Xero doesn't match the bank statement, it's typically due to missing, duplicated, or incorrectly entered transactions.
- Verify the reconciliation date exactly matches your bank statement end date
- Look for transactions with incorrect dates that may fall outside the reconciliation period
- Ensure all bank fees, interest, and charges are recorded in Xero
- Check for foreign exchange differences if you deal with multiple currencies
- Use the 'Reconcile Later' option for unclear or disputed transactions
- Verify opening balances are correct from previous reconciliation
- Check for uncleared checks or deposits in transit
2. Integration and sync problems
1) Ecommerce platform sync failures
Integration issues with platforms like Shopify, Amazon, or other marketplaces can result in missing sales data, incorrect inventory levels, or failed order imports. These problems often stem from API changes, authentication issues, or mapping errors.
How to fix it:
- Reconnect your platform in Xero or your integration tool (e.g., Webgility)
- Check for platform-specific sync error messages
- Update login credentials and permissions
- Verify sync filters (dates, order statuses, etc.)
- Update the integration app to the latest version if available
2) Third-party app integration issues
This Xero issue arises when apps fail to connect or post data due to broken links, revoked permissions, or rate limits.
How to fix it:
- Disconnect and reconnect the problematic app completely
- Check API usage limits in your Xero developer console and upgrade if necessary
- Verify app permissions in Xero's 'Connected Apps' settings
- Update the third-party app to the latest version
3) Data mapping and categorization errors
Incorrect account assignments, wrong tax codes, or improper product mappings can cause financial data to appear in the wrong categories, affecting reporting accuracy.
How to fix it:
- Review and update account mapping settings in your integration apps
- Create or modify bank rules for automatic transaction categorization
- Use Xero's bulk update features for correcting multiple items simultaneously
- Review and test mapping rules with sample transactions
3. Invoicing and payment issues
1) Invoices not sent or being received by clients
Invoices may not reach clients due to email configuration problems or branding template issues.
How to fix it:
- Check your invoice branding theme for email settings
- Whitelist Xero's email domain
- Ask your client to check spam/junk folders
- Test by sending an invoice to your own email
- Check Xero's email delivery logs for bounce-back messages
2) Online payments not working
Stripe, GoCardless, or PayPal connections may be misconfigured or disconnected, causing payment links to fail.
How to fix it:
- Reconnect the payment service in Xero under Settings > Payment Services
- Ensure online payment is enabled in your invoice template
- Test the payment link before sending invoices
- Verify Stripe/GoCardless/PayPal account is active
- Check for any payment gateway service outages on their status page
4. Performance and technical issues
File upload and attachment problems
Files may fail to upload due to size restrictions, unsupported formats, or browser compatibility issues.
How to fix it:
- Convert files to PDF, PNG, or JPG
- Keep file sizes under 25MB
- Upload via desktop instead of mobile
- Try uploading smaller files in separate batches
5. Ecommerce-specific troubleshooting with accounting automation solution - Webgility
1) Multichannel sales data discrepancies
When selling across multiple platforms, data may not sync correctly, leading to missing transactions or duplicate entries.
How to fix it:
- Verify all sales channels are connected in Webgility
- Check date ranges for data synchronization across all platforms
- Review marketplace-specific settings and configurations in Webgility
- Identify and manually add any missing transactions (Webgility does it for you through its automation features and connection to various sales channels and accounting platforms)
- Set up automated rules for different marketplace requirements
- Configure proper tax handling for each sales channel
2) Inventory synchronization problems
Stock levels may not match between ecommerce platforms and Xero, causing inventory discrepancies and incorrect cost calculations.
How to fix it:
- Check inventory sync settings in Webgility configuration
- Verify product mapping between all platforms is accurate
- Set up proper inventory tracking methods in Xero
- Use Webgility’s real-time inventory sync
- Audit stock levels across platforms
Also read: 5 Tips for Keeping Inventory Accurate in Real-Time
3) Settlement and payout reconciliation
Matching gross sales to net deposits can be challenging when dealing with multiple marketplaces and payment processors with different settlement schedules.
How to fix it:
- Map gross sales to net deposits systematically for each platform by integrating Webgility
- Account for all marketplace fees and commissions accurately
- Set up dedicated accounts for different settlement types
- Use automated matching rules for regular, predictable settlements
When to contact Xero support
Even with a robust knowledge of Xero, some issues require escalation to official support. This section helps you recognize when to seek direct help and which alternative resources can complement your troubleshooting.
1. Recognizing system-wide problems vs. user-specific issues
Before contacting support, determine whether your problem is isolated or affecting other users.
- Navigate to Xero Status page lists current outages and known issues
- System-wide problems often include login outages, feed disruptions across multiple banks, or errors affecting reports and transactions platform-wide
- User-specific issues usually result from misconfiguration, expired credentials, or data-entry mistakes on your end
If the problem is system-wide, you may just need to wait for a resolution. If it’s unique to your account, proceed with contacting Xero support.
2. Account-specific problems only Xero can resolve
Certain types of account issues can’t be resolved through documentation or community help:
- Locked-out administrator access with no backup user
- Suspended or deactivated subscriptions
- Account ownership disputes or transfer requests
- Data restoration after accidental deletions
- Historical feed access or audit log recovery
- Duplicate or corrupted organization files
In these cases, only Xero Support has the necessary tools and security clearance to act.
3. Alternative support resources
While waiting on official customer/live support or in situations where issues are user-specific, these resources can save time:
Xero central (Knowledge Base)
- Visit Xero Support page for expert help
- Includes how-to articles, troubleshooting guides, and platform updates
Xero community forums
- Ask questions and browse peer answers at Xero Community
- Useful for discovering workarounds or common fixes
Certified advisor assistance
- If you're working with a Xero-certified accountant or bookkeeper, they often have faster access to support escalations and deeper knowledge of setup/configuration
- You can find advisors through the Xero Advisor Directory
Third-party troubleshooting resources
Integration partners like Webgility often maintain their own Help Center that address Xero sync issues.
Finding the balance for your Xero accounting
After looking at different challenges faced by Xero users, one thing is clear - Xero users might often struggle with the manual effort required to keep accurate, up-to-date financial records for multichannel ecommerce businesses.
This is where integrating an automation platform like Webgility can offer a powerful solution to many of the common pain points Xero users face.
Ready to eliminate core Xero issues? This is how Webgility makes it possible-
- Reduce manual data entry errors by syncing online orders from Shopify, Amazon, eBay, and more into Xero with complex transactions like shipping costs, sales tax and refunds automatically
- Simplify reconciliation by matching sales, deposits, and fees automatically
- Update stock levels and pricing across every platform, preventing overselling and stockouts
- Handle accounting across several storefronts and currencies with localized compliance
If you want to scale confidently across borders and channels, Webgility + Xero is your all-in-one answer!
FAQs
What are the main challenges users face when using Xero?
Common challenges include issues with bank feeds, reconciliations, inventory management, manual reporting, and integrations. Understanding these challenges is crucial for effectively using Xero and maintaining accurate financial records.
How can I manually initiate a sync in Xero?
Go to the Xero integration panel and click ‘Sync now’ in the top-right corner. This will sync all enabled bank feeds. For specific areas like Bill Pay or Expense Management, you can click ‘Refresh Xero’ to sync those particular sections.
How can I prevent Xero sync problems?
Set up sync alerts and notifications, regularly update integration settings, use test transactions before full sync, and choose the appropriate sync method (manual or auto) based on your specific business needs.
- Reassure users that most issues are easy to fix with the right steps
- Leveraging Webgility support for ecommerce-specific issues
- Encourage proactive review and use of built-in Xero tools
- Link to Xero support and additional resources