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Private patients: card, EFTPOS and Stripe

A Stripe payout arrives net of fees, so it is smaller than the invoices behind it. A terminal card settlement arrives gross, and the merchant fee is billed later. The allied health template holds each in its own clearing account and posts the Stripe fee to a merchant fee expense, which leaves one bank line to match per payout.

Key facts

Who pays
The payment processor, not a funder: an online card processor on one rail, and the bank behind a standalone merchant facility on the other12
Deposit shape
One payout per automatic payout schedule, covering the transactions settled in that batch, with a gross, a fee and a net recorded against each one2
Time to funds
Two business days initial settlement timing for an Australian Stripe account, then the account's own payout schedule1
Fee timing
Netted from each Stripe payout, and billed monthly on a standalone terminal facility12
Published domestic card fee
1.7 percent plus A$0.30 per charge, with Stripe stating that its fees include GST4
Breakdown file
The itemised payout reconciliation report, one row per transaction carrying the payout id, the gross, the fee and the net2
Revenue account in the allied health template
400 Clinical services, private patients, as GST free income12
Fee account in the allied health template
604 Merchant and claiming fees, with GST on expenses12

Two private rails, and only one of them is gross

A private patient is the only payer who settles on the spot, which sounds like the easy case and is not. The money still arrives through a processor, and the processor decides what the bank line looks like. A terminal settles the day gross and bills its fee later. An online card processor pays out net, with the fee already gone before the practice sees the money. The invoices in the practice system are the same in both cases, so the whole difference lands in the bank feed.

What each private rail hands the bank feed1226
What arrivesTerminal card settlementOnline card payout
Bank lineThe day's approved card takings, grossOne payout per schedule, net of fees
Fee timingBilled monthly by the acquiring bankNetted from each payout, per charge
Clearing account in the allied health template106 EFTPOS clearing107 Online payments clearing
BreakdownThe terminal's settlement totals for the dayItemised payout reconciliation report, one row per transaction
What breaks the matchThe monthly fee debit, which has no invoice behind itThe fee, which makes the payout smaller than the invoices

Why a payout is smaller than the invoices behind it

Stripe's published Australian rate is 1.7 percent plus A$0.30 for a domestic card and 3.5 percent plus A$0.30 for an international one, and the pricing page states that its fees include GST. The same page carries a note that lower pricing applies from 1 Oct 2026, so the rate to work from is the one on the practice's own account. The fee comes off each charge inside Stripe rather than off the payout as one line, so a payout covering four consultations is short by four separate fees, none of which appears on any invoice.

Stripe payoutA Stripe payout drawn whole: four patient card payments receipted to the online payments clearing account, the processing fees withheld, and the smaller amount that reaches the bank.Settled 28 Aug 2026Stripe payoutPrivate consultation,standard sessionA$200.00107 Online paymentsclearingPrivate consultation, shortsessionA$150.00107 Online paymentsclearingInitial assessment, extendedA$250.00107 Online paymentsclearingTelehealth review, privateA$100.00107 Online paymentsclearingFees withheldA$13.10Bank lineA$686.90The four charges less the processing feesequal the payout to the cent, and the feesare four per charge amounts rather than onededuction.
Plate 1One Stripe payout, drawn whole. The fees are already gone by the time the bank line appears.

The arithmetic holds on both sides. The trouble is that Xero is handed the net figure and asked to match it against invoices raised at the gross amount, and the obvious fix, editing the invoice, is the one that breaks.

The settlement that matches the day, and the debit that does not

A standalone terminal is the mirror image. The bank line equals the day's approved card takings, so the deposit reconciles against the receipts with no fee in sight. The fee turns up weeks later as a single monthly debit with no invoice behind it, and the canonical template posts that debit to the merchant fee account rather than netting it against revenue.

Terminal card settlementA terminal card settlement drawn whole: three card payments at the desk receipted to the EFTPOS clearing account, no fee withheld, and a bank line equal to the day's takings.Settled 28 Aug 2026Terminal card settlementPrivate consultation, gappaid at the deskA$130.00106 EFTPOS clearingPrivate consultation, gappaid at the deskA$130.00106 EFTPOS clearingReview appointment, paid infullA$88.00106 EFTPOS clearingBank lineA$348.00No fee is withheld, so the settlement equalsthe day's card takings and the merchant feearrives as its own debit in the followingmonth.
Plate 2The same day on a terminal. The settlement equals the takings, and the fee arrives on its own later.

The Xero rejection a fee on the invoice produces

The tempting fix is to add the processing fee to the invoice so the invoice total matches the payment that was taken. Where the invoice has already gone to Xero as approved, Xero holds it at its old total and refuses the larger payment. Zanda's troubleshooting note describes the cause plainly.

the payment you are exporting is worth more than the invoice's total already recorded in Xero5

The way back it sets out has two halves, one for the invoices already stuck and one for the export order that stops it happening again.

  1. For an invoice already approved in Xero, post the payment at the invoice's own recorded value, excluding the fee, and record the processing fee separately as a bank or processing fee expense reconciled through the same clearing account the card payments run through.
  2. Going forward, export invoices as late as possible, after the payment and its processing fee have both been taken, so the invoice and the payment reach Xero at the same total.
  3. Keep the fee out of revenue either way. Netting it against income understates total sales on the activity statement and hides what the rail costs the practice.

The report that splits a payout into its charges

Stripe publishes a report whose stated purpose is this exact match, and it is the file a bookkeeper should be working from rather than a bank statement narration.

helps you match the payouts you receive in your bank account with the batches of payments and other transactions that they relate to2

  • The automatic payout id, the one field that groups a batch of transactions into the payout that actually reached the bank.
  • The charge id, which ties a line back to the payment that was taken.
  • The invoice number, which Stripe fills only where the charge sits against a Stripe Billing invoice, so a practice invoicing from its own system matches on the charge id or on metadata it set itself.
  • Gross, fee and net for every transaction, so the fee total is read off the file rather than worked out by hand.
  • The reporting category, the field the report groups a settlement batch's transactions by.
  • The trace id, the reference the bank generates for the payout, which is how a bank line can be found again.
  • Withheld tax, which Stripe describes as sales tax, VAT or GST withheld, and says is already included within the fee column.

One limit is worth knowing before a practice leans on the report. It covers automatic payouts. For an instant payout Stripe says it cannot identify which transactions are inside the payout, which leaves the practice matching those against its own transaction history.

When the money lands, and when the report does

Stripe's settlement timing table gives Australia an initial settlement timing of two business days and no separate default after that, and the payout schedule itself is an account setting: daily, weekly, monthly or manual. Report data for a day's activity is normally available around midday the following day. So the bank line can land before the file that explains it, which is the same ordering problem a Medicare payment run has.

That gap is the argument for a clearing account rather than matching a payout straight to revenue. The clearing account holds the gross receipts from the moment the practice system records them, and the payout is a transfer out of it. What is left sitting in the account is the money the processor is still holding, which is a figure a practice owner can check against the processor's own dashboard.

GST on the revenue, and GST on the fee

In the allied health canonical template a private consultation posts to account 400, Clinical services, private patients, as GST free income. The ATO sets three conditions for a health service that is not a medical service: it is a listed health service, it is performed by a recognised health professional in that listed service or by their assistant under the supervision conditions the ATO sets out, and it is generally accepted in that profession as being necessary for the appropriate treatment of the recipient of the supply. Who handed the money over is not one of the three, and the ATO says a supply that meets the definition keeps its treatment where a third party pays the practitioner on the patient's behalf. A report or a training session posts to its own account as taxable, whichever card was tapped. Supervision sits on the same account by the template's default, and that account's own note asks a practice to confirm it, because one reading treats supervising another practitioner as a service to that practitioner rather than a health service and an ATO interpretative decision is cited as pointing the other way. A take home product is taxable by default too, with the template carrying an item level override to GST free for Schedule 3 medical aids, because the ATO treats goods a patient takes home as GST free only where they are a necessary part of the health service supplied at the same time.

The fee is the other side of the same deposit. The template posts a processing fee to 604, Merchant and claiming fees, with GST on expenses, and Stripe's pricing page states that its fees include GST. That puts a small input tax credit inside an otherwise GST free revenue stream, which is worth expecting on the activity statement rather than being surprised by.

The clearing account Xero will not let you reconcile

The clearing account pattern is what the vendors' own documentation points at, and Xero gives you no reconcile screen for the account it asks you to create. The request to reconcile clearing, control and non bank accounts has sat on Xero's product ideas board since 2012, and Xero's own answer in 2022 was direct.

To be upfront, we don't have any plans to develop the ability to reconcile clearing, control and non-bank accounts in the near future.7

The bookkeepers on that thread are blunt about what it costs them. One describes taking up to three hours a month to reconcile a clearing account in a spreadsheet, work their previous ledger did not ask for. Another says reconciling from extracted files is not viable, because it takes far too long and leaves no record inside Xero. A practice consultant writing about batch payouts puts the same problem from the practice side.

if fees have been taken out before the money hits your account, the deposit won't even match the total of those invoices8

What Ledger Map does with it

Ledger Map holds one standing map for the practice, approved before anything syncs. A private card line resolves to its account and its tax rate through that map. A payout is posted as one balanced document set: the receipts against the clearing account, the fee against the merchant fee expense, and the transfer that leaves one exact match against the bank line. Anything the map cannot resolve becomes a question with the options laid out, rather than a quiet posting nobody sees.

None of the treatments on this page are choices Ledger Map made. The accounts and the tax codes come from the canonical template the practice starts from, and the practice approves the map before an invoice moves. You can see the shape of it on how it works, and compare the other private rails on the funders hub and the Tyro EFTPOS and HealthPoint page.

Questions

  • Why is my Stripe payout less than the invoices it covers?

    The processing fee comes off each charge before the payout leaves Stripe. Stripe's published Australian rate is 1.7 percent plus A$0.30 for a domestic card, so a payout covering four consultations is short by four fees, not one. The payout is correct and the invoices are correct, and the difference is a fee that appears on neither.

  • How do I record Stripe fees in Xero?

    Record the fee as an expense on the payout, not as a line on the invoice. The allied health canonical template posts the fee to 604, Merchant and claiming fees, with GST on expenses, while the patient payments sit in 107, Online payments clearing. The payout then reconciles as the clearing transfer less the fee.

  • Why does Xero say the payment amount exceeds the amount outstanding on this document?

    Xero says this when the payment being exported is worth more than the invoice total it already holds, which usually means a card processing fee was added to the payment after the invoice was exported and approved. Post the payment at the invoice's own value in Xero and put the fee in its own expense line instead.

  • Can I claim the GST on a Stripe fee when the consultation is GST free?

    Stripe states that its Australian fees include GST, and the canonical template codes the fee with GST on expenses, which puts an input tax credit inside a GST free revenue stream. That is a question for the practice's BAS agent on the practice's own figures, and it is why the template carries the tax code rather than leaving the fee in revenue.

  • Why does an EFTPOS settlement match the day's takings but a Stripe payout does not?

    The difference is fee timing. A standalone terminal facility settles the day gross and bills its merchant fee monthly, so the deposit equals the receipts. An online card processor nets its fee from each payout, so the deposit is short. The invoices are the same and the bank lines are opposite, which is why the template gives the two rails separate clearing accounts.

Sources

Open questions

  • Stripe's Australian pricing page gives 1.7 percent plus A$0.30 for a domestic card while Xero's own App Store listing for Stripe gives 1.75 percent plus A$0.30, so the rate that matters is the one on the practice's own account rather than either published figure.
  • Stripe's pricing page also carries a note that lower pricing applies from 1 Oct 2026 for domestic cards and from 1 Apr 2027 for international ones, without publishing the new rates, so the figures on this page are the ones in force when it was read and the worked payout is arithmetic rather than a current quote.
  • Stripe publishes an initial settlement timing of two business days for Australia and no separate default after that, and the payout schedule is an account setting, so no published figure settles the lag for any one practice.
  • The Zanda troubleshooting article now serves from a different address than the one recorded in the research corpus, and it carries no last updated date, so its wording could move without notice.
  • The dispute and chargeback posting and the cents level rounding line in the canonical template are conventions rather than sourced rules, and the template says so in its own notes for a BAS agent.
  • The bank narration a payout or a merchant settlement carries could not be confirmed from a primary source, so descriptor patterns are learned from the practice's own feed rather than written into the map.
  • The ranking order of the current top results for this query is unverified. The search budget was exhausted on the research pass and again on the fact check pass of 3 Sep 2026, so the answer landscape in the brief is assembled from the ranking pages themselves and from the corpus's recorded search snippets rather than from a live results page.
  1. Payouts

    Stripe. Retrieved 2 Sep 2026.

    primary

  2. Payout reconciliation report

    Stripe. Retrieved 2 Sep 2026.

    primary

  3. Payout schedules frequently asked questions

    Stripe. Retrieved 2 Sep 2026.

    primary

  4. Pricing, Australia

    Stripe. Retrieved 2 Sep 2026.

    primary

  5. Troubleshooting Xero exports

    Zanda. Retrieved 2 Sep 2026.

    primary

  6. Stripe on the Xero App Store

    Xero. Retrieved 2 Sep 2026.

    primary

  7. Reconciliation: ability to reconcile clearing, control and non bank accounts

    Xero product ideas. Retrieved 2 Sep 2026. Source updated 14 Sep 2022.

    secondary

  8. Halaxy batch payments and Xero reconciliation

    Time Well Spent. Retrieved 2 Sep 2026. Source updated 20 Jul 2026.

    secondary

  9. GST and health, other health services

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  10. GST and health, supply of services through a third party

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  11. GST and health, goods supplied as part of a GST free health service

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  12. Allied health by funding source, the canonical template

    Ledger Map. Retrieved 2 Sep 2026.

    primary

Review

Last reviewed 2 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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