Problems
Cliniko refund does not show up in Xero
Cliniko records a refund by reversing the invoice into a credit note of its own, or as a negative payment against account credit. Its integration article documents invoices and allocated payments crossing to Xero and names neither, so the Xero side keeps the sale closed. Entering it takes a credit note on the reversed line's own account and tax rate, or a release of held credit.
Key facts
- How Cliniko records a refund of a paid invoice
- Press Reverse on the invoice, and Cliniko builds a credit note that reverses every item by applying a negative quantity1
- How Cliniko refunds money that was never applied
- A negative number in the payment source field, matching the amount being handed back from the patient's account credit3
- The two things Cliniko can do with a refund
- Record money going back to the patient, or convert the payment into account credit rather than paying it out2
- What Cliniko documents crossing to Xero
- All invoices and allocated payments, and a payment only once it is allocated, which is why an unallocated payment is not seen in Xero4
- What Cliniko documents not crossing
- Credit allocations, which do not appear in Xero, and payments made using account credit, which leave the invoice open in Xero4
- What the integration article does not name either way
- A reversal, a credit note or a refund. None of the Cliniko articles read for this page says whether one reaches Xero4
- What another practice system says plainly
- PracSuite states that refunds are not included in its Xero sync and have to be adjusted in Xero by hand8
- Where the balance drifts
- Cliniko pushes each allocated payment into the clearing account as a debit, and a refund nobody entered leaves that debit standing6
- Where the refund is entered in Xero
- In the Sales menu, select Invoices, open the Awaiting payment tab, open the credit transaction being refunded and click Add cash refund11
- The liability the templates hold unapplied money in
- Account 245, Customer deposits and credits held, posted BAS excluded until the money is applied, forfeited or handed back12
What Cliniko sends to Xero, and what stops at the door
The integration is one directional and selective, and Cliniko is precise about the parts it documents. It pushes all invoices and allocated payments across, and a payment only once it is allocated, so an unallocated payment sitting on a patient file is not seen in Xero at all. Credit allocations do not appear in Xero. A payment made using account credit is not accepted by Xero, so the invoice syncs across and then sits there open, even though Cliniko has closed it.
Read those rules together and a pattern shows up. What the article names travelling is the sale and the money that settles it. The things that reduce what a patient owes are either documented as not travelling or are not named at all, and a refund is in the second group.
| What happens in Cliniko | What Cliniko says reaches Xero | What that leaves you |
|---|---|---|
| A payment allocated to an invoice | It is pushed across once it is allocated | The sale and its payment agree on both sides |
| A credit allocated to an invoice | Credit allocations do not appear in Xero | The invoice closes in Cliniko and stays open in Xero |
| A payment made using account credit | Not accepted by Xero, and the invoice stays open there | An open invoice in Xero that nobody actually owes |
| An invoice reversed into a credit note and refunded | The integration article names invoices and allocated payments and stops there | Nothing documented to point at, which is how a refund goes missing |
| An invoice archived, with its payments | Archiving is documented as a Cliniko action with no Xero step | The Xero invoice and its payment are both still standing |
The reversal Cliniko creates, and where it stops
Cliniko does have a refund of its own. Find the invoice, press Reverse, and Cliniko builds a credit note that reverses every item on the invoice by applying a negative quantity, then offers to create the credit and the refund together. Refund part of it and you adjust the items first. Money that was never applied to an invoice takes the other path: a negative number in the payment source field, matching the amount handed back from account credit.
So the practice system has done a careful job, and the trail stops at the integration. Cliniko documents pushing invoices and allocated payments to Xero and names nothing else. None of its articles read for this page mentions a reversal, a credit note or a refund crossing, or an error, a queue or a warning, which is why practices find these weeks later while chasing a balance.
Two refunds that look the same at the desk
Before anything is entered in Xero, one question decides what to enter. Had the money being handed back ever been applied to an invoice? Applying money to an invoice is the moment it stops being a liability and becomes reported revenue, so the two cases move different accounts.
- Money still held and never applied: an unused session pack, a booking fee for an appointment that never happened, a credit put on a file in error. Nothing was reported as a sale, so nothing has to be unreported.
- Money already applied to an invoice: a gap paid twice, a session billed and then reversed, an invoice the patient paid in full that a funder later settled as well. This is revenue that has been reported, and reversing it takes a credit note.
- A refund covering both at once. There is no single obviously correct posting, so it is two documents on the amounts each covers rather than one document for the total.
The two documents Xero needs instead
Money that was never applied is released from the liability it was sitting in. In the canonical allied health template that is account 245, Customer deposits and credits held, posted BAS excluded, so the liability falls by the amount handed back and no revenue and no tax move. One payment out, one bank line to match, no invoice touched.
Money that was already applied takes the pair any reversal of revenue takes. Raise a credit note against the same contact for the lines being refunded, on the same account and the same tax rate the original line carried. Allocate it to the invoice so the balance moves. Then refund whatever credit balance is left, from the account the money physically left. Xero starts that last step from the invoice list rather than from the contact: in the Sales menu, select Invoices, open the Awaiting payment tab, open the credit transaction and click Add cash refund. Reconciling a refund in Xero walks the screens.
The tax rate a credit note has to copy
A credit note copies the line it reverses rather than picking a rate of its own. In the canonical template a private clinical session posts to account 400, Clinical services, private patients, as GST free income, and a take home item posts to account 422, Products and equipment sales, as taxable. Refund a session and a splint on one transaction, and the reversal is two lines at two rates, exactly as the original invoice was.
The reason the treatment holds is the ATO's own test for a health service that is not a medical service: a listed health service, performed by a recognised health professional in that service or by their assistant under the supervision conditions the ATO sets out, and generally accepted in the profession as necessary for the appropriate treatment of the recipient of the supply. A refund does not change any of the three, so the reversal carries the treatment the sale carried.
Picking a rate by hand is where a refund quietly changes the tax on a period that has already been reported, which is a harder thing to find than a missing refund.
What the drift looks like in the ledger
While the refund is unrecorded, four balances are wrong at once, and none of them looks obviously wrong on its own. No single report shouts, and the numbers only stop adding up at the end of a quarter.
Cliniko describes the mechanism behind the last row plainly. When it pushes payments across it is creating debits, so the balance rises, and reconciling the deposit creates the matching credit that wipes the debt off. A refund removes money one of those debits is still counting, and nothing on the Cliniko side takes it back out.
Finding the refunds already missed
If this page describes your practice, there is a backlog rather than a single refund. Five checks turn it up, and they work on a month you can still open.
- List the refunds in Cliniko for the period. Cliniko shows them as negative numbers in the daily payments report and the payment summary report, so they are countable even though nothing about them crossed.
- Put that list beside the credit notes in Xero for the same dates. A refund with neither a credit note nor a release of held money behind it has not been recorded.
- Read the clearing total for the month from the Cash Summary report, which is where Cliniko points for the payments it pushed across in a date range. Reports open from the Reporting menu, under All reports.
- Look for invoices that are closed in the practice system and open in Xero. Payments made with account credit produce exactly that, and they sit next to the refunds in the same backlog.
- Work oldest first, and check the lock date before posting. A refund dated inside a closed period is a question for the accountant rather than a document to redate quietly.
Archiving the invoice is not a refund
The most common way this gets worse is the fix that feels tidiest. Archive the invoice in Cliniko, and the invoice and the payments attached to it are archived with it, which looks from the inside exactly like a reversal. Cliniko's article on archiving says nothing about Xero, and a bookkeeper who works on this pair for a living says why that matters.
You may assume that when you archive an invoice in Cliniko, that action results in the invoice being removed in Xero also, but that's not the case.9
Her point is that the integration does not carry it, so the Xero invoice has to be voided by hand, and the evidence you would have used is archived on the side that had it. The same post makes the credit case just as plain: allocate a credit in Cliniko and you still apply it in Xero yourself. An archived Cliniko invoice still in Xero is that case in full.
What it costs when nobody catches it
The cost is not the refund. It is that receivables, the balance sheet and the practice's own sense of what is owed drift together, slowly, and only surface when somebody is paid to unpick it.
Higher accounting or bookkeeping fees if your trusted professionals have picked up the problems.9
That is the same register as a clearing account that will not clear and invoices paid by account credit staying open. One unwind that does not arrive, multiplied by a year.
What Ledger Map does with it
Ledger Map holds one standing map for the practice, approved before anything syncs. A refund is read as the shape it actually is: money released from the held credits liability where it was never applied, or a credit note on the reversed line's own account and tax rate plus a refund against that credit note where it was. Each deposit is posted as one balanced document set, which leaves one exact match in the bank feed.
A refund spanning both cases is not guessed. It is raised as a question with the candidate postings shown, for somebody who knows the arrangement to answer. None of the treatments here are choices Ledger Map made: the accounts and tax codes come from the canonical template the practice starts from, and the practice approves the map first. You can see the shape of it on how it works.
Questions
Do refunds sync from Cliniko to Xero?
Cliniko's help centre does not say. Its integration article documents all invoices and allocated payments being pushed across, and names credit allocations and payments made with account credit as things that do not appear in Xero. A reversal, a credit note and a refund are not named either way, and PracSuite states the same gap for its own product in as many words.
How do I show a refund in Xero?
As one of two documents, entered by hand. Money already applied to an invoice takes a credit note against the same contact, on the same account and tax rate as the line it reverses, allocated to the invoice and then refunded from the account the money left. Money that was never applied is released from the held credits liability instead.
What do refunds go under in Xero?
The reversal goes back to the account the original line used, at the tax rate that line carried, rather than to an account of its own. In the canonical allied health template a private session sits in account 400, Clinical services, private patients, and a take home item in account 422, Products and equipment sales. Money that was never applied sits in account 245, Customer deposits and credits held.
Why is my invoice still showing as paid in Xero after I refunded it in Cliniko?
Because the sale and its payment crossed and the reversal did not. Xero holds the invoice in the state the last document it received left it in, so it stays closed until a credit note is raised against the same contact and allocated to it.
Why will my clearing account not come back to zero after a refund?
Cliniko pushes each allocated payment into the clearing account as a debit, and the bank deposit reconciles it away. A refund takes back money one of those debits is still counting, so the balance holds a residue for every refund nobody entered. Entering the refund against the same account is what clears it.
Does archiving an invoice in Cliniko remove it from Xero?
No. Cliniko documents archiving as removing the invoice from Cliniko, along with any payments attached to it, and says nothing about Xero. A bookkeeper who works on this pair writes that the integration does not carry the action, so the Xero invoice has to be voided by hand.
Read next
- Xero how toHow to reconcile a refund in Xero
- ProblemsInvoices paid by account credit stay open in Xero
- ProblemsArchived Cliniko invoice is still open in Xero
- ProblemsClearing account will not clear in Xero
- Xero how toHow to reconcile a credit note in Xero
- Practice systemsCliniko Xero integration: what syncs, what does not
- HubProblems
Sources
Open questions
- Whether a Cliniko reversal, credit note or refund reaches Xero is not stated in any Cliniko article read for this page. The integration article documents invoices and allocated payments crossing and names nothing else, so the page states what Cliniko documents rather than asserting a sync behaviour the vendor has not published. This is the item that keeps the page at draft.
- Xero's refund article gives the entry point and the Add cash refund step. It does not say what a refund of money that was never applied should be coded to, so the account this page names for that case comes from the canonical template rather than from Xero. The procedure and its screens are owned by /xero/reconcile-a-refund.
- Whether archiving a payment in Cliniko reverses a debit already pushed into the Xero clearing account is not stated by either Cliniko article, so the page names the balance to check rather than the behaviour to expect.
- The Festival Bookkeeping post carries no publication or last updated date, so its wording could move without notice.
- Whether a card refund put back through the same terminal reduces a later settlement or arrives as its own outgoing line depends on the merchant facility, and no source read here settles it.
- The bank narration a refund line carries is not stated by any source read for this page, so no descriptor pattern appears here and the map learns them from the practice's own feed.
- Recording a refund, giving money back to the patient
Cliniko. Retrieved 3 Sep 2026. Source updated 19 Jun 2025.
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- Delete or refund a patient's account credit
Cliniko. Retrieved 3 Sep 2026. Source updated 3 Jan 2025.
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- Integrate Cliniko with your Xero account
Cliniko. Retrieved 3 Sep 2026. Source updated 28 Jul 2026.
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- Reconcile in Xero when using the Cliniko integration
Cliniko. Retrieved 3 Sep 2026. Source updated 28 Jul 2026.
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- GST and health, other health services
Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.
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Review
Last reviewed 4 Sep 2026 by Shane
General information for Australian allied health practices, not tax advice. Confirm a treatment with your BAS agent or accountant before you post it.
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