Reconciling your settlements in QuickBooks or Xero is typically a straightforward process, but occasional issues may require a little troubleshooting. This article provides a systematic guide to help you find and resolve common reconciliation problems.
Preliminary Checks
Before diving into deeper troubleshooting, it's always a good idea to perform these initial checks:
Verify the Deposit: First, confirm that the deposit from your sales channel has actually been received in your bank account. A simple failed bank feed may be the cause of the issue.
Check Link My Books Status: Once you've confirmed the deposit, check that the settlement is available and has been successfully sent from Link My Books. If the settlement is not in your Link My Books dashboard, refer to our help article: Some of my settlements are missing
Xero - Why the Transaction Isn't Matching
If the bank deposit has been received but a corresponding match isn't automatically suggested in Xero, the issue is likely due to the transaction being categorised differently than expected.
Check for Awaiting Invoices
While a bank deposit typically shows an automatic match for a corresponding invoice, you may sometimes need to manually search for it.
From your Xero dashboard, navigate to the Awaiting Invoices section to search for the settlement in question.
Check for Bills
On some occasions, a settlement may be sent as a bill rather than an invoice. This can happen if your Amazon fees and advertising costs are greater than your sales amount, for example. We have a dedicated help article for this instance: Why are some of my settlements being sent as bills instead of invoices to Xero?
The bills section can be accessed from your Xero dashboard.
Incorrectly Reconciled or Duplicated Entries
It is possible that a settlement was reconciled incorrectly against the wrong bank deposit, or that a duplicate entry was created.
To check this, go to Bank Statements and search for the payment. If it has been reconciled incorrectly, you'll be able to 'Remove & Redo' the reconciliation.
Settlement Shows as "Sent" in Link My Books But Doesn't Appear in Xero
In some cases, a settlement may show a "Sent" status in Link My Books but you cannot find the corresponding invoice or bill anywhere in Xero. This can happen when:
The Xero connection experienced a temporary issue during the send (e.g. an API timeout or rate limit), causing the settlement to be marked as sent in Link My Books without the transaction being fully created in Xero.
An account or tax code used in the settlement was deleted, archived, or changed in Xero after the settlement was configured, causing Xero to silently reject the transaction.
The settlement was sent to a different Xero organisation than the one you are checking.
To resolve this:
In Link My Books, open the settlement and check the Events tab for any error messages or warnings that may indicate what went wrong.
Verify your Xero connection is active by going to Settings > Account Settings and checking the connection status. If it shows as disconnected, reconnect and try again.
Use the Rollback feature to undo the settlement, then resend it. This will create a fresh transaction in Xero. See: Rollback Feature: How It Works
Check your Accounting & Taxes mappings to ensure all accounts and tax codes are still valid and active in Xero.
Tip: If you see the settlement as "Sent" but it's not in Xero, always try a rollback and resend first — this resolves the issue in most cases.
QuickBooks - Why the Transaction Isn't Matching
Incorrect Bank Account Assigned
It's a good idea to double-check that you have the correct bank account assigned within Link My Books for your QuickBooks integration. If the wrong bank account is assigned, the settlement entry will not appear in the correct bank feed for reconciliation.
To check this: In Link My Books, navigate to Accounts & Taxes > QuickBooks Bank Accounts.
Incorrectly Reconciled or Duplicated Entries
It's not unheard of that a settlement has been reconciled against a deposit incorrectly. You can check if this has happened by heading your Banking tab and use the search or filter options to locate the specific transaction. You'll then be able to manually find the corresponding invoice.
This can be checked under Bank Transactions. You'll need to locate the transaction and un-reconcile it.
Once located you can Undo the selected transaction to un reconcile it.
Still Not Showing?
QuickBooks Bank reconciliation feature will only suggest matches for the last 3 months, if the payout is older than this then you will need to manually search for the matching journal.
Still Unsure?
If you've worked through this checklist and are still unable to reconcile the transaction, please get in touch with our support team, and we can take a closer look for you.
If you have any questions about this article or feedback on how we could make it better please reach out to the support team via the blue chat icon on the bottom right of the page or via email to [email protected].