How do I split a bank statement line in Xero?

Open the credit on the reconcile screen, break it into coded rows instead of accepting it whole, and give each row its own account and tax rate. For a settlement that arrived net, that is two rows: the gross against the funder's clearing account at BAS Excluded, and the fee against merchant and claiming fees at GST on Expenses. The rows have to add to the credit.

Why is my payout smaller than the invoices it paid?

Because the processor took its fee before paying out. Stripe's payout reconciliation report shows the batch of transactions behind each payout with gross, fee and net columns, so the difference is a stated figure rather than a variance to hunt for. The gross belongs against the clearing account and the fee belongs in an expense account.

Why does my clearing account not return to nil after a card payout?

Usually because the credit was coded whole. The payments posted into the account at gross and the deposit came out at net, so the fee stays behind as a residue that grows with every payout. Recode the deposit as two rows, the gross out of the clearing account and the fee to the expense account, and the balance closes.

Do I split a HICAPS or Tyro Health settlement the same way?

The canonical template records both of those as billing their fees separately each month rather than netting them, so the settlement posts gross and the monthly bill is its own transaction. Whether HICAPS Digital nets its fee, and whether Tyro EFTPOS settles gross or net, are both unverified in the research, so check a real statement before assuming either shape.

Is splitting a line the same as find and match?

No. Find and match ties one bank transaction to several payments that already add up to it, which Cliniko's guide describes for a clinic syncing payments into Xero. Splitting a line is for a credit that is not all one thing, most often because a fee came out of it before the money moved.

Xero how to

Split a bank statement line in Xero

Split the line into two coded rows. Put the gross figure the settlement report shows against the funder's clearing account at BAS Excluded, and the fee against merchant and claiming fees at GST on Expenses. The two rows net to the credit in the feed, the clearing account clears in full, and the fee is named rather than left as a variance.

Key facts

What a split is for: One statement line reconciled against more than one account, so a credit that is not all one thing stays one line in the bank account¹
The case that needs it: A settlement that arrives net. The canonical template records online card payouts as arriving net of fees, so the credit is smaller than the invoices it pays¹
The two rows: The gross to the funder's clearing account at BAS Excluded, and the fee to 604 Merchant and claiming fees at GST on Expenses¹
Where the fee figure comes from: The settlement report, not an estimate. Stripe's payout reconciliation report carries gross, fee and net columns for each reporting category and for each transaction in the itemised download²
The arithmetic the split satisfies: Gross less fee equals the credit in the feed, which is also why the clearing account returns to nil instead of holding the fee as a residue¹
Which rails need it: The rails that take their fee out of the settlement. The allied health canonical template gives its online payments rail a fee component posting to 604, and records HICAPS terminal and Tyro Health claiming fees as billed separately each month¹
What the split does not touch: The revenue leg. The account and tax rate for the service sit on the invoice the payment closes, so a split only sets the settlement leg and the fee leg¹
Why the fee carries GST on Expenses: The template treats merchant and claiming fees as GST inclusive charges, so the expense account claims the GST inside the fee rather than treating the whole fee as net¹
What the generic answer covers: Find and match, which Cliniko's guide describes as finding and matching a single bank transaction to multiple payments. It handles many invoices, not a fee taken out of them⁵
Tax withheld inside a fee: Stripe's reports carry a withheld tax column described as sales tax, VAT or GST withheld, already included within the fee column, so the fee figure is the inclusive one³

Two jobs share the word split

People searching for this are usually holding one of two problems, and they need different answers. The first is one credit that paid several invoices, where nothing is missing and the job is to tie the line to the set of payments behind it. The second is one credit that is not all the same kind of money: part of it belongs against invoices, and part of it is a charge somebody took out before the money moved.

Only the second one needs the line broken into coded rows. The first is find and match, and the practice system vendors describe it well. Cliniko's guide tells a clinic that find and match will help you find and match a single bank transaction to multiple payments, then tells you to confirm the deposit is the amount you were expecting against the clearing account report. That sentence is where the second problem starts, because a netted settlement is not the amount you were expecting.

Which one you are holding

The two questions that both get called splitting a line⁵¹

What you are looking at	What it needs	What the line ends up as
One credit that closes several invoices, and the invoices add to it exactly	Find and match, or one batch deposit built from the remittance	One statement line matched to a set of payments
One credit that is smaller than the invoices it covers, because a fee came out first	The line broken into coded rows, one for the gross and one for the fee	One statement line carrying two rows that net to the credit

The rest of this page is the second row of that table, because it is the one the generic answers leave out and the one a clinic taking card payments meets every payout.

Why a netted settlement is different

When a processor pays out, it settles a batch of transactions and takes its fee on the way through. Stripe's payout reconciliation report exists for exactly this: it matches the payouts you receive in your bank account with the batches of payments and other transactions that they relate to, grouped by reporting category, and both the summary and the itemised download carry gross, fee and net columns.

Those three columns are the whole page. The gross is what the invoices were paid. The fee is a cost the practice incurred. The net is what the bank feed shows. Coding the credit whole to the clearing account posts the net where the gross belongs, and the difference then sits in the clearing account as a residue nobody can name at month end.

One payout, drawn whole

Plate 1An illustrative card payout, split into the two rows that net back to the credit in the feed.

The plate is the split. One row carries the gross against the clearing account, one row carries the fee against the expense account, and the credit sitting in the feed is what the two come to. Nothing is estimated, because the settlement report already states all three figures.

The steps, in order

Outside Xero, in the processor or funder portal. Open the settlement or payout report behind the credit and read three figures off it: the gross the payments came to, the fee that was taken, and the net that was paid.
The reconcile screen for the bank account the credit landed in. Check that the net on the report equals the amount on the statement line before touching anything, because a difference here is a second problem rather than a fee.
The statement line itself, on that reconcile screen. Split the line rather than coding it whole, so it can carry more than one row instead of forcing the whole credit into one account.
The transaction details behind the statement line. Code the first row to the funder's clearing account for the gross figure, at BAS Excluded, because the revenue was posted when the invoice was raised.
The second coded row on that same transaction. Code the second row to 604 Merchant and claiming fees for the fee, as a negative amount at GST on Expenses, so the two rows net back to the credit.
The same transaction, before it is saved. Check that the gross less the fee equals the statement line. The split is finished when those rows add to the credit, and not before.
The account transactions report for the clearing account. Open the clearing account afterwards and confirm it returned to nil for that settlement, which is the test that the gross leg carried the right figure.
The file attached to the reconciled transaction. File the settlement report against the transaction, so the fee figure can be traced in six months without opening the portal again.

Three legs, three tax rates

The reason this trips people is that a netted payout touches three accounts with three different treatments, and only two of them are in the split. The revenue leg was set when the invoice was raised. In the allied health canonical template a private patient consultation lands on 400 Clinical services, private patients, and the ATO's conditions for a listed health service decide its tax rate, not the card that paid it.

The settlement leg is the gross row. The template posts every clearing component at BAS Excluded, because the money has already been earned and reported and the clearing account is only holding it between the invoice and the bank. The fee leg is the second row, at 604 Merchant and claiming fees with GST on Expenses, because the template treats merchant and claiming fees as GST inclusive charges.

Which rails need a split at all

This is a lookup rather than a judgement. The canonical template records a fee timing per rail and, where a rail carries a fee of its own, the account that fee posts to. The rail that needs a split is the one that takes its fee out of each settlement. A rail billed monthly needs no split, because the fee arrives as its own direct debit and is coded straight to the expense account. A rail that carries no fee at all, such as a Medicare or an NDIA payment run, pays the claim gross.

Fee timing per rail, as the allied health canonical template records it¹

Rail	Fee timing in the template	What the deposit needs
Online payments processor, the template's Stripe rail	Netted per settlement	A split: the gross to the clearing account, the fee to merchant and claiming fees
HICAPS terminal health fund claims	Billed separately each month	No split: the daily settlement reconciles to the gross fund benefit alone
Tyro Health claiming settlements	Billed separately each month	No split: the settlement posts gross and the monthly bill is its own transaction
A standalone merchant facility	Recorded as billed monthly, flagged in the template as an assumption to confirm	Check the practice's own merchant agreement before assuming either shape

What goes wrong when the line is coded whole

The clearing account stops clearing. Posting the net where the gross belongs leaves the fee behind as a balance that grows every payout and cannot be traced to a claim.
The fee disappears from the profit and loss. A cost the practice genuinely paid does not reach an expense account, so the margin on card payments looks better than it is.
The GST on the fee is left unclaimed, because there is no expense line for Xero to carry it on.
Someone eventually clears the residue to a suspense account or writes it off, which hides a recurring cost inside a one-off adjustment.

None of those show up as an error. They show up as a clearing balance that a bookkeeper cannot explain, months later, with the settlement reports long since scrolled off the portal.

Doing it the same way twice

A split done by hand is fine once and expensive weekly. Two things make it repeatable. The first is writing down which account the fee row goes to and at what rate, so two people reconciling in the same ledger do not pick different accounts. The second is a bank rule keyed on the credit's own narration, which can pre-fill the coded rows and leave a person to check the figures rather than type them.

The narration itself is worth learning from the practice's own feed rather than copying from a guide, because it varies by bank and by product. The bank rules for funder deposits page covers the rule side, and reconcile a clearing account covers reading the balance the split is meant to keep at nil.

What Ledger Map does with a netted deposit

Ledger Map holds one standing map for the practice, approved before anything syncs. It does not auto reconcile. For a rail the approved map records as netted, it posts one balanced document set for the deposit, with the gross against the clearing account and the fee against the expense account the map names, and leaves one exact match in the bank feed for a person to accept.

Where the settlement report and the payments do not agree, that becomes a question with the options laid out rather than a quiet posting. Nothing on this page is a treatment Ledger Map picked: the accounts, the tax rates and the fee timings all come from the canonical template a practice starts from, and the practice signs off the map first. The product walkthrough shows the map and the question queue, and private patients paying by card covers where this deposit comes from.

Questions

How do I split a bank statement line in Xero?
Open the credit on the reconcile screen, break it into coded rows instead of accepting it whole, and give each row its own account and tax rate. For a settlement that arrived net, that is two rows: the gross against the funder's clearing account at BAS Excluded, and the fee against merchant and claiming fees at GST on Expenses. The rows have to add to the credit.
Why is my payout smaller than the invoices it paid?
Because the processor took its fee before paying out. Stripe's payout reconciliation report shows the batch of transactions behind each payout with gross, fee and net columns, so the difference is a stated figure rather than a variance to hunt for. The gross belongs against the clearing account and the fee belongs in an expense account.
Where does the fee go when a settlement arrives net?
In the allied health canonical template it goes to 604 Merchant and claiming fees at GST on Expenses, because the template treats merchant and claiming fees as GST inclusive charges. Stripe's reports also carry a withheld tax column, described as sales tax, VAT or GST withheld and already included within the fee column.
Why does my clearing account not return to nil after a card payout?
Usually because the credit was coded whole. The payments posted into the account at gross and the deposit came out at net, so the fee stays behind as a residue that grows with every payout. Recode the deposit as two rows, the gross out of the clearing account and the fee to the expense account, and the balance closes.
Do I split a HICAPS or Tyro Health settlement the same way?
The canonical template records both of those as billing their fees separately each month rather than netting them, so the settlement posts gross and the monthly bill is its own transaction. Whether HICAPS Digital nets its fee, and whether Tyro EFTPOS settles gross or net, are both unverified in the research, so check a real statement before assuming either shape.
Is splitting a line the same as find and match?
No. Find and match ties one bank transaction to several payments that already add up to it, which Cliniko's guide describes for a clinic syncing payments into Xero. Splitting a line is for a credit that is not all one thing, most often because a fee came out of it before the money moved.

Sources

Open questions

Xero Central returned nothing readable to an automated fetch on 3 September 2026 for the split bank transaction article, and the Xero developer site returned nothing readable for the bank transactions API page. The steps on this page therefore say where the work happens in plain terms rather than naming a Xero menu path, and the Xero Central article is cited here as unverified.
The current answer landscape was not sampled, at drafting or at review on 3 September 2026, because the web search budget was spent both times. The top five on google.com.au for the target query, the People Also Ask set and what an answer engine cites today were not read, so what this page adds is stated against the vendor pages that were readable rather than against the live result set.
The template's merchant and claiming fees account asks a practice to confirm that each rail's fee is actually GST inclusive before the GST on Expenses default is relied on, so the fee row's tax rate is a default to check rather than a settled treatment.
Stripe's own payouts page does not state in so many words that a payout is net of fees. The gross, fee and net structure this page relies on comes from the payout reconciliation and balance summary report pages instead, and neither prints a last updated date.
Whether HICAPS Digital nets its fee from settlement is unverified in the research corpus, and whether Tyro EFTPOS card settlements arrive gross or net is unverified as well. Both are stated here as things to check against a real statement rather than as a treatment.
The template's standalone merchant facility rail records a monthly fee as a generic assumption rather than a sourced fact, and asks for the practice's own merchant agreement to be checked. A practice whose facility nets daily would need the split on that rail too.
Whether a single Xero statement line can be split across two saved documents rather than two coded rows on one document was not confirmed against Xero's own documentation, so the page states the arithmetic the rows have to satisfy rather than a screen sequence.
The bank narration a card payout carries is not published and varies by bank, so the bank rule section says to learn it from the practice's own feed rather than naming a string.

Allied health by funding source, the canonical template
Ledger Map. Retrieved 3 Sep 2026.
primary
Payout reconciliation report
Stripe. Retrieved 3 Sep 2026.
primary
Balance summary report
Stripe. Retrieved 3 Sep 2026.
primary
Payouts
Stripe. Retrieved 3 Sep 2026.
primary
Reconcile in Xero when using the Cliniko integration
Cliniko. Retrieved 3 Sep 2026. Source updated 28 Jul 2026.
primary
Other health services, GST and health
Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.
primary
Reconcile a split bank transaction, a Xero Central article
Xero Central. Retrieved 3 Sep 2026.
unverified

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.

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