Xero how to
Two payments on one invoice in Xero
Record two payments on the one invoice, each dated when that half was taken, and post each to the account for the rail it will settle through. The invoice closes on the day of service. Later, each bank line is matched against the account that held its half, so neither half is held up by the other.
Key facts
- Where a payment type points
- Each payment type can be pointed at its own Xero account from a drop down, and that setting overrides the default payment account7
- The setting still required underneath
- A default Xero payment account has to be set as well, or payments do not sync to Xero at all7
- When a payment reaches Xero
- Only once it is allocated to an invoice in the practice system, so an unallocated payment is not visible on the Xero side1
- The other shape of integration setting
- One Xero payments account for the whole practice, separate from the sales account, where every exported payment lands8
- What that vendor tells its users to do
- Export the payments to a clearing account in Xero, then code the settlement's receive money transaction to that account8
- What Xero does with too much money
- The exporting vendor's own article says Xero does not permit a payment larger than the invoice amount, so an excess cannot be stretched onto the invoice8
- Where the fund half waits
- Account 104, HICAPS clearing, an asset account of Xero bank type posting at the BAS excluded tax type12
- Where the card half waits
- Account 106, EFTPOS clearing, on the same footing, for a terminal card settlement that is not routed through a claiming service such as HICAPS or Tyro12
- How the clearing account is chosen
- One clearing account per settlement rail rather than per funding source, because the rail is what produces the bank line and the funding source stays on the revenue lines12
- Where the revenue sits
- Account 403, clinical services private health fund benefit, at the GST free income tax type in the canonical template12
- When each fund has to pay
- Each fund calculates the day's approved amount less its authorised cancellations and pays it within 10 business days, by direct credit to the bank account the practice nominated11
- Why the fund settlement arrives gross
- No fee is charged to process health fund or Medicare Easyclaim transactions, and card processing is charged monthly to a nominated account4
- The second payment that can take months
- Where the patient pays only the gap, a cheque in the provider's name goes to the patient, and the 90 day cancellation scheme behind it names allied health professionals, optometrists and dentists as ineligible6
- Editing once both payments are on
- A sync returns "This document cannot be edited as it has a payment or credit note allocated to it", and the change is made in Xero rather than pushed from the practice system9
One invoice, two payments, two arrival dates
A health fund claim and the patient's gap on the same appointment are two payments, not one. The fund approves its benefit on the terminal, the patient taps for the rest, and the invoice is settled in full before they leave. What has not happened yet is the money arriving. Two payers each owe the practice their share, on two different runs, and the invoice should not sit half open while they land.
- The invoice is one document for the whole fee, and it closes when the payments on it add up to that fee.
- Each payment carries its own date, its own payment type, and its own account on the Xero side.
- The patient's half rides the day's card settlement. The fund's half settles on its own run.
- Neither half is a part payment in the Xero sense, because nobody underpaid. Two payers each paid their share of the same fee.
Where each payment posts, and why not the bank account
Point each payment at the account for the rail it will settle through, rather than at the operating bank account. The canonical allied health template keeps one clearing account per rail, not one per funding source. It gives a fund benefit claimed through HICAPS account 104, HICAPS clearing, and a card settlement from the practice's own merchant facility account 106, EFTPOS clearing. Both are asset accounts of Xero bank type posting at the BAS excluded tax type, because money on its way to the practice is not a supply.
The tax treatment is a separate leg and the invoice already decided it. A private health fund benefit posts to account 403, clinical services private health fund benefit, at the GST free income tax type in the canonical template, and a private patient's own share posts to account 400. The revenue line carries the treatment. The payment leg carries none of it.
| The appointment | Taken at the desk | Arrives later | Where each half waits |
|---|---|---|---|
| Fund member with a gap to pay | The gap, by card on the terminal | The approved fund benefit, on the fund settlement run | The card half in EFTPOS clearing, the benefit in HICAPS clearing |
| Private patient who claims the rebate back | The whole fee, by card | Nothing on the practice side, because the patient pays in full and the rebate goes back to them | One half only, in EFTPOS clearing |
| Gap only patient claim, paid to the provider through the claimant | The gap, by card | A cheque in the provider's name sent to the patient, with no electronic fallback for an allied health practice | The gap in EFTPOS clearing, the rebate outstanding until the cheque or the transfer arrives |
| Scheme participant paying a difference themselves | The participant's own share | The scheme or plan manager's payment for the claimed lines | Each half in the account for the rail that pays it |
Why the two halves land apart
The claiming terminal settles at 21:30 VIC or NSW time each day, a time the practice can move, and that closes the day's claiming. It does not set the payment date. Each fund works out the day's approved amount less the cancellations it authorised, then has 10 business days to pay it by direct credit into the nominated account. The card half runs on the merchant agreement's schedule instead. No fee is charged to process a health fund or Medicare Easyclaim transaction, and card processing is billed monthly, so the fund settlement arrives gross.
What your practice system does with the second payment
None of this works unless the practice system sends the two payments to two accounts, and the systems answer that differently. One lets each payment type carry its own Xero account, which overrides the default payment account, and still needs a default set underneath or nothing syncs at all. The other sends every exported payment to a single Xero payments account, separate from the sales account, and tells its users to make that a clearing account and code the settlement's receive money transaction to it.
- Check the integration settings in the first week rather than the first quarter. A payment type left on the default drops both halves in the same place, and the aggregate looks fine while nothing ties out.
- A payment reaches Xero only once it is allocated to an invoice in the practice system, so a payment sitting unallocated is invisible on the Xero side and the invoice stays open.
- Where the system offers one payments account only, the second payment can still be moved in Xero, but that is a manual step per invoice rather than a setting.
- A sync that changes an invoice a payment is already allocated to comes back refused, so the account is fixed in Xero rather than in the practice system.
The steps, in order
Two of these six steps happen once, at set up, and the other four happen on the day. The first one carries the rest: if nobody names who settles each part, what follows is guesswork.
- Read the invoice and name who settles each part: the fund or scheme benefit, and the patient's own share. (Outside Xero, on the practice system's invoice)
- In the practice system's Xero settings, point each payment type at the account for the rail it settles through, rather than leaving both on the default payment account. (Practice system, Xero integration settings)
- Record both payments against the one invoice, each dated the day that part was taken. The invoice closes once the two add up to the invoice total. (Sales, Invoices, Awaiting payment)
- Check that the fund benefit is sitting in account 104, HICAPS clearing, and the card payment in account 106, EFTPOS clearing. (Accounting, Chart of accounts)
- When the day's card settlement lands, match that bank line as a transfer out of the EFTPOS clearing account for the settled amount. (Bank account, Reconcile)
- When the fund benefit settlement lands on its own run, match that bank line as a transfer out of the HICAPS clearing account. (Bank account, Reconcile)
Reconciling each bank line against its own account
Neither settlement is matched back to the invoice. The invoice closed at the appointment, and matching a deposit to it a second time would count the same consultation as revenue twice. Each settlement is matched instead as a transfer out of the account that has been holding that half of the money since the day of service.
The day's card line usually covers many appointments at once, so it clears the EFTPOS clearing account by the sum of that day's gaps rather than by one invoice's worth. The fund settlement does the same for the benefits, and reconciling card settlements covers the card side in full.
The gap only claim, where the second payment is months away
One case stretches this shape a long way. Where the patient pays only the gap and the claim is lodged to be paid to the provider through the claimant, a cheque in the provider's name is sent to the patient's last known address, and it is the patient's job to bring it in. There is a scheme that cancels an unbanked cheque after 90 days and pays by electronic transfer. Services Australia names allied health professionals as ineligible for it.
So one invoice carries a payment taken at the desk and a second one that can take a quarter to arrive. The gap behaves like any card payment. The rebate does not: nothing is settling on a rail, and a balance sitting in a settlement account for three months reads as a reconciliation failure rather than as what it is. Whether to carry it as a receivable instead is a practice decision, and this page states both.
Two payments is not a part payment, an overpayment or a batch
Four things look similar on the reconcile tab and want four different answers. The distinguishing question is simple: did somebody pay less than they owed, or did two people each pay what they owed?
- A funder that paid less than the invoice is a part payment, and the balance left behind is a decision about who still owes it.
- Money above the invoice total is an overpayment, and a payment larger than the invoice is not permitted, so the excess cannot be stretched onto the invoice.
- One deposit covering many invoices is a batch, which is a matching problem rather than a question about how many payments an invoice carries.
- A deposit that arrived net of a fee is a split bank statement line, where the gross goes to the account holding it and the fee to an expense account.
Checking it at month end
Both accounts should empty. A balance that survives a fortnight is a payment recorded against a settlement that did not arrive, and it points at one of a short list of causes.
- A claim cancelled on the terminal the same day reverses the benefit before it settles, so the payment stays on the invoice and the balance stays behind it.
- A card payment recorded on a day the terminal did not settle sits until the next settlement sweeps it up.
- A payment type left on the default account puts both halves in one place, where the total still looks right and neither deposit can be traced.
- A payment allocated in the practice system but not yet exported leaves the invoice open in Xero while the practice system shows it closed.
The month end check is the one every settlement account needs, and reconciling a clearing account sets it out, including what an aged balance is telling you.
What Ledger Map does with it
Ledger Map posts one balanced document set per deposit, built from the funder's own report, and leaves one exact match in the bank feed for a person to accept. An appointment that two payers settled produces two of those sets on two different days, each against the account for the rail that paid it, while the invoice itself is closed once, on the day of service.
Which payment type reaches which account is part of the standing map a practice approves before anything posts, so it is decided once and in the open rather than found in the second year. How it works walks through that approval, and setting up a clearing account covers the accounts the two halves wait in.
Questions
Can one invoice have two payments in Xero?
Yes. Payments are separate records, each with its own date and its own paid to account, and the invoice closes once they add up to the invoice total. More money than the invoice is a different matter: a payment larger than the invoice amount is not permitted, so an excess is dealt with separately rather than stretched onto the invoice.
How do I reconcile two payments to one invoice in Xero when they arrive on different days?
Post each payment to the account for the rail it settles through, so the invoice closes on the day of service. Then match each bank line, when it lands, as a transfer out of the account that held that half. The bank lines are matched to those accounts, not to the invoice a second time.
Should the fund benefit and the patient gap go to the same account?
Only if they settle together, and usually they do not. The gap rides the day's card settlement while the fund benefit settles on its own run, so one account holding both leaves a balance that cannot be tied to either deposit. Two accounts let each bank line prove itself.
What if my practice system only offers one payments account?
One system points each payment type at its own Xero account and that setting overrides the default, while another sends every exported payment to a single payments account and asks you to make that a clearing account. With a single account, the second payment can be moved in Xero by hand, and that change is made in Xero because a sync to an invoice a payment is already allocated to comes back refused, so it is a step per invoice rather than a setting.
What happens when the second payment is a Medicare rebate months later?
Where the patient pays only the gap and the claim is paid to the provider through the claimant, a cheque in the provider's name goes to the patient. The 90 day scheme that cancels an unbanked cheque and pays the practitioner by electronic transfer names allied health professionals, optometrists and dentists as ineligible, so an allied health practice waits on the cheque itself. The gap behaves like any card payment. How the rebate is carried in the meantime is a practice decision worth settling with the bookkeeper before the first one arrives.
Read next
Sources
Open questions
- No google.com.au ranking, AI Overview or People Also Ask data could be observed for this query on 3 Sep 2026, because the session's web search budget was exhausted, so the answer landscape in the brief is argued from the sources that could be read rather than from a ranking.
- Xero Central settles where the invoice list sits, and the step names that path. Xero's own article for this task was not read: central.xero.com returned an empty document on 3 Sep 2026 and the developer documentation renders client side, so the mechanics of two payments on one invoice rest on the vendor sources instead.
- Whether the day's fund benefits arrive as one deposit or one deposit per fund could not be confirmed from a primary source, which the canonical template already flags on the account itself.
- The 10 business days is the outer limit the provider agreement sets, not a published settlement standard, so the day a practice actually sees the benefit is worth reading off its own feed.
- Where the gap is tapped on the same terminal that carried the claim, the card half settles through that terminal's own merchant facility rather than a standalone one. The canonical template models the two rails separately and this page follows it, so the account for the card half is the one for the rail that settles it.
- Whether a card facility bills its processing fees monthly or nets them from each settlement is a term of the practice's own merchant agreement, and the canonical template marks its monthly assumption as unconfirmed for a standalone terminal.
- Whether a practice system that offers a single payments account can route two payment types on one invoice to two accounts is not stated by either vendor article read for this page.
- How a gap only rebate should be carried while it is outstanding, as a receivable or in a settlement account, is a question for the practice and its bookkeeper. Both readings are stated here and neither is resolved.
- The timeline on this page is an illustrative appointment rather than a practice's data, and the elapsed times on it are what the sources state rather than a reading of any one clinic's feed.
- The 90 day pay doctor cheque scheme, archived capture of the page as last updated 3 March 2022
Services Australia. Retrieved 4 Sep 2026. Source updated 3 Mar 2022.
primary
- Sync payment types in Cliniko to specific clearing accounts in Xero
Cliniko. Retrieved 3 Sep 2026. Source updated 18 May 2026.
primary
- HICAPS provider agreement terms and conditions, clauses 5.5 to 5.7
HICAPS. Retrieved 3 Sep 2026.
primary
Review
Last reviewed 3 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.
Guided onboarding
Run one real month before you go live.
Sign up, connect Zanda and Xero, and replay a month you already closed. The map is reviewed with whoever owns the books, and nothing posts until you approve it.
Every practice starts from a template. Nothing posts until the map is approved.