The simplest way to know your Xero or MYOB integrations are working is to check them once a month, on purpose, before month-end close. You don't need technical skills. Compare the count and total of invoices, bills, payments and credit notes in each source system with what landed in Xero or MYOB, read the connector's error log, spot-check the coding, look at your clearing accounts, scan for duplicate contacts and items, and confirm every connection is still authorised. Write down what you found. Once it's routine, the whole check takes about a quarter of an hour, and it catches problems while they're still a few records rather than a few months.
Why integrations fail quietly
Most integrations don't break with a bang. A connector stops sending one type of record, or a token expires on a weekend, or someone renames a tracking option in one system and not the other. The app's dashboard still says "connected". Invoices still appear in Xero. Nobody notices that credit notes stopped arriving three weeks ago, or that one job's costs are going to an uncoded line.
By the time someone spots it, there's a backlog to untangle without creating duplicates. If this sounds familiar, our page on integrations that only half work describes the common patterns.
Before you start: list what's connected
Do this once. For each integration, write down the source system (job system, CRM, online store, payroll or inventory app), what it sends to Xero or MYOB, where its error log lives, and which user authorised it. If nobody knows who connected it, that's your first finding.
The monthly check, step by step
Run this on the same working day each month, before you close the period. Use last month's dates.
1. Compare counts and totals by record type
This is the most important step. In the source system, run a report of last month's records. In Xero or MYOB, filter the same records for the same dates. Compare two numbers for each type: how many, and the total value.
- Sales invoices: count and total including GST.
- Supplier bills: count and total.
- Payments received and made: count and total.
- Credit notes: count and total, plus how many are still unallocated.
Counts match but totals don't: look for changed amounts or rounding. Totals match but counts don't: look for records combined or split, such as one payment across several invoices. Neither matches: something failed to send, or someone keyed records straight into the accounts.
Keep the comparison in a spreadsheet: one row per record type, one column per month.
2. Read the connector's error or sync log
Open each integration's log and look for anything that failed, was skipped or is "pending". Clear every item, not just the recent ones. A single failed record from six weeks ago is often the reason a total doesn't match.
A recurring error such as "account code not found" means a mapping problem that will keep happening until it's fixed.
3. Spot-check tracking categories, jobs and account codes
Pick five records at random from last month and open them in Xero or MYOB. Check that each line has the right account code, tax code and tracking category (in Xero) or job (in MYOB).
Then run a profit and loss filtered by tracking category or job, and look for an "unassigned" or blank column. Any value sitting there is income or cost that your job or department reports are missing. The usual cause is a new job or cost centre set up in one system and not the other. If you need more than two tracking categories in Xero, see our post on Xero tracking category limits.
4. Check suspense and clearing accounts
Many integrations post to a clearing account while they wait to match things up, for example payments from a payment gateway or deposits that cover several invoices. Run the account transactions report for each suspense or clearing account and check the balance.
A clearing account should come back to zero, or close to it, each month. A growing balance means transactions are stuck, and your reports are out by that amount.
5. Look for duplicate contacts and items
Integrations often create a new contact when they can't find an exact match: "ABC Pty Ltd" and "ABC Pty Ltd." become two customers, each with half the history. The same happens with inventory items and products.
Sort your contact list by name and scan for near-duplicates created in the last month. Do the same for items if your integration creates them. Merge or archive duplicates in the accounts, and fix the name in the source system so it doesn't happen again.
6. Confirm every connection is still authorised
Integrations connect using an authorisation that one of your users granted. That authorisation can lapse, and when it does, the connector simply stops sending.
- Xero: in Xero, go to your organisation's Settings and open Connected Apps. Check that every app you rely on is listed and still connected. Xero's developer documentation says that if an app doesn't refresh its access within 60 days, the user has to authorise it again. This mostly affects integrations that run occasionally or have quietly stopped.
- MYOB: MYOB's API support centre says refresh tokens last up to one week from when they were issued, so an integration that stops running for more than a week will need reconnecting. MYOB also changed its permissions on 1 September 2026 and says an Administrator user of the company file must approve the connection. If anything stopped around then, read why MYOB integrations stopped working after the API change.
Also check that the user each app was authorised under still exists. If a staff member who connected an app has left and their user was removed, the app can lose its access. Vendors change these rules from time to time, so check the current Xero or MYOB help if something doesn't match what's described here.
7. Record the result
Write one line per integration: the date, whether it reconciled, what didn't match, and what was done about it. Keep it next to your month-end checklist. It answers "how long has this been wrong?" when something does go wrong.
What to do when it doesn't reconcile
Don't fix totals with a journal and move on. A journal hides the problem and it will come back next month.
- Find the missing or extra records. Export both lists for the record type that doesn't match, sort by date and reference, and compare them side by side. The differences are usually a handful of records.
- Work out why each one failed. Check the log entry for each. Common causes are an unmapped account or tax code, a missing contact or item, a locked period in Xero or MYOB, an expired connection, or a record entered in the accounts by hand.
- Fix the cause before resending. Correct the mapping or reconnect the app first. Resending without fixing the cause just fails again.
- Resend carefully. Before you resend anything, check it isn't already in the accounts. Resending from the source system after someone keyed it in by hand creates a duplicate.
- Tell the people who caused it. If a renamed job or new cost centre was the cause, they need to set it up in both places next time.
If the differences are large, go back months, or keep returning after you've fixed them, the problem is no longer a monthly tidy-up.
When it's worth getting help
For many businesses, a marketplace connector plus this check is all you need. If you have one or two integrations, the counts match most months, and the occasional failure is easy to trace, keep doing the check and save your money.
It's worth getting help when:
- The same mismatch comes back every month after you've fixed it, which usually points to a design or mapping problem rather than a one-off.
- Nobody knows how an integration works or who built it, so failures can't be traced.
- The check takes far longer than it should, because there are several systems, several entities, or thousands of records to compare by hand.
- The history is already wrong, with months of missing, duplicated or miscoded records that need cleaning up before any fix will hold.
That's the work we do in Xero and MYOB integration repair: find out why records don't match, fix the cause, clean up the history, and add proper error alerts and a daily comparison so nobody has to rely on a person noticing. If you'd like the whole picture mapped first, across every system and process, our Process & Systems Audit costs $5,000 and produces a written report. For background on connectors, custom builds and migrations, see the Xero and MYOB integration and migration guide.
Frequently asked questions
How do I know if my Xero integration is working?
Compare last month's count and total of invoices, bills, payments and credit notes in the source system with the same records in Xero. Then check the connector's error log and confirm the app is still listed under Settings, Connected Apps. If the numbers match and the log is clear, it's working.
Why does my Xero app keep disconnecting?
Common reasons are an app that hasn't refreshed its access within 60 days (Xero then requires the user to authorise it again), the user who authorised it being removed from the organisation, or someone disconnecting it in Connected Apps. Reconnect it as a user with the right access, then check what was missed while it was down.
Why do I have to reconnect my MYOB integration?
MYOB's refresh tokens last up to a week, so an integration that stops running for longer needs reconnecting. MYOB's permissions change on 1 September 2026 also meant many integrations had to be updated and approved again by an Administrator user of the company file.
How often should we reconcile integrations with Xero or MYOB?
Monthly, before month-end close, is a sensible minimum. If you send a lot of records or rely on the integration for payroll or billing, a quick weekly look at the error log is worth adding.
If your monthly check keeps turning up the same problems, or you'd rather not rely on someone remembering to run it, book a free initial chat. We'll tell you plainly whether a set-up fix will do or the integration needs more work.