Practice systems
Halaxy Xero integration: sync, fees, duplicates
Halaxy sends invoices, payments and expenses into Xero automatically once the connection is made, mapped by fee category, expense category and payment method. The sync moves records; it does not reconcile. Batched takings, the fee taken out of a card payment and rebates that record themselves are what leave a balance behind. Post each settlement through a funder clearing account and match one bank line.
Key facts
- Direction
- Invoices, payments and expenses sync from Halaxy into Xero automatically once the connection is made2
- Account mapping
- Revenue by Halaxy fee category, expenses by expense category, and invoice and expense payments by payment method, each to a chart of accounts you choose, with a default behind every one1
- Cost of a patient payment taken in Halaxy
- 1.5 to 1.9 percent per transaction, plus a 75c to 1 dollar fee, on the Silver and Bronze bands3
- Cost of the platform
- Free, with credits at A$0.15 to A$0.22 including GST and subscription features from 25 credits a month3
- Cost of a claim through HICAPS Digital
- Set by the scheme: no fee on nib selected modalities, HBF, icare, NDIS, WorkSafe Victoria and WorkCover Queensland, 1.45 percent of the approved claim for the Transport Accident Commission, and 10c an approved invoice for Medicare and veterans affairs6
- What bookkeepers report breaking
- Merchant fees, batched takings, identical amounts matching the wrong invoice, and setup errors that compound4
- Clearing accounts in the allied health template
- 104 HICAPS clearing and 107 online payments clearing, both bank type and BAS excluded9
What the sync sends to Xero
The Halaxy connection is a push into Xero. Once a practice authorises it, invoices, payments and expenses raised in Halaxy appear in Xero without anyone exporting a file, and the connection is made at group, clinic or individual practitioner level. Setup then maps revenue by Halaxy fee category, expenses by expense category, and invoice and expense payments by payment method, each to a chart of accounts you choose. That last mapping is the setting the pattern below rests on.
- Invoices raised in Halaxy, as Xero sales invoices.
- Payments recorded against those invoices, to the Xero account chosen for invoice payments.
- Expenses entered in Halaxy.
- The mapping itself, set once per connection at group, clinic or practitioner level.
What it does not send back
By default the sync runs one way. Records created in Halaxy appear in Xero, and records created in Xero do not appear in Halaxy. Two way syncing is a checkbox in the Xero sync preferences, and Halaxy limits it to invoice payments. Switch it on and a payment added or assigned in Xero updates the Halaxy invoice, but you cannot then edit that payment from Halaxy: the change has to be made in Xero and flows back from there.
The practical consequence is the same either way. A correction made in Xero is a correction to a copy. The bookkeeping firm that works in these files puts it plainly: corrections belong in Halaxy first, and Xero second.
A sync is not a bookkeeping system. Integration moves information. It does not replace reconciliation, account mapping, GST review or bookkeeping judgement.5
Claimed, reported, and unverified
Four of the five pages that answer this query today are Halaxy's own support articles, and a support site that refuses automated readers is also refusing the answer engines. So the table below keeps three things apart: what a page anyone can open actually states, what a bookkeeping firm reports from practice files it works in, and what this page does with the gap between them.
| What Halaxy documents | What bookkeepers report | How this page treats it | |
|---|---|---|---|
| Sync direction | One way by default, with two way syncing available as a preference and limited to invoice payments | Corrections belong in Halaxy first, because the sync carries them one way | Read as one way into Xero unless the practice has turned two way syncing on |
| Account mapping | Revenue by fee category, expenses by expense category, and invoice and expense payments by payment method | Small setup errors compound, and surface months later as a balance nobody can explain | One standing map, approved before anything posts, with the reason on every row |
| Tracking categories | Not mentioned in the Xero articles | Not discussed | An open question, not a feature claim |
| Batched deposits | Batched daily payouts show one deposit a day on the bank feed while each invoice syncs on its own | Batching the day's collection into one bank credit often complicates the reconciliation | One balanced document set per deposit, leaving one exact match in the bank feed |
| Merchant fees | Auto Payment fees sync either as an expense or as a negative invoice line, to a revenue, expense or liability account you choose | Mishandled fees are a frequent cause of reconciliation delay once volumes rise | Gross to the clearing account, fee to its own expense line with GST on expenses |
| Duplicate payments | Income counted twice when a synced payment meets the same money on the bank feed, which Halaxy cannot see | A duplicate points at a workflow or sync issue, so find the record that carries the real activity first | Raised as a question with the options laid out rather than posted twice |
| Cost | Platform free, credits at A$0.15 to A$0.22 including GST, subscription features from 25 credits a month | Not discussed | The cost of the accounting connection itself is not published |
Where the merchant fee breaks the match
A patient payment taken inside Halaxy carries a processing cost of 1.5 to 1.9 percent per transaction plus a 75c to 1 dollar fee on the Silver and Bronze bands. A claim sent through HICAPS Digital carries the fee its own scheme carries: nothing on the schemes HICAPS lists as free, 1.45 percent of the approved claim for the Transport Accident Commission, 10c an approved invoice for Medicare and veterans affairs. The invoice in the practice system is for the full amount, because that is what the patient owes and what the fund approved. The bank credit is for something less.
That difference has to land somewhere, and the two places it usually lands are both wrong. Netted into revenue, it understates income and quietly moves a taxable expense into a GST free sales figure. Left in a matched deposit as a rounding difference, it disappears from view and takes the audit trail with it. The bookkeeping firm names mishandled fees as a frequent cause of reconciliation delay once transaction volumes rise.
Claims lodged outside the claiming channel
The harder cases are the claims that do not go through the terminal or the digital claiming channel. Workers compensation and NDIS work is often lodged with the insurer or the plan manager directly, which means the money arrives on its own timetable, in its own deposit, with its own paperwork, and with nothing in Halaxy expecting it. The firm working these files names claims handled outside the claiming channel as a cause of delayed payment, unclear remittance advice and manual identification.
Each of those funders is its own rail with its own lag and its own breakdown file, which is why they get their own pages rather than a line on this one. Start with HICAPS for fund benefits at the desk, Medicare bulk bill for the rebates that record themselves, and card and online payouts for anything settled net of fees.
Why batching the day's takings makes it worse
Banking the day's collection as one credit looks like less work, and for the person banking it, it is. For the person reconciling it, one credit covering many payment methods is a puzzle with no key: the fund benefit, the card takings and the patient gaps arrive on different days and carry different fees, so the total in the bank matches nothing in the ledger.
Duplicates, and rebates that record themselves
Halaxy's own answer to income counted twice names the bank feed, not the practice system. Payments sync from Halaxy as income, then the same money arrives on the bank feed and is coded as income a second time, because Halaxy cannot see that feed. The vendor's fix is a clearing account, and a chart of accounts for payments that is not the revenue account. The two way guide names a second cause: where a rebate or a scheduled payment already records itself in Halaxy, marking it paid in Xero as well produces the pair.
- Find the record that carries the real activity. One of the two is a copy, and deleting the wrong one loses the claim reference.
- Correct it in Halaxy, then let the correction reach Xero, rather than editing the Xero copy and leaving the two files disagreeing.
- Check whether an automated Halaxy transaction and a synced payment are both switched on for the same payment type, because that is the condition that produces the pair.
- Watch the clearing balance afterwards. A duplicate receipt clears an invoice no funder paid, so the balance moves the wrong way and stays there.
The clearing account that will not clear
A clearing balance is a question, not a problem in itself. It says money has been recognised that the bank has not delivered yet, which is exactly what should be true during a funder's lag. What it should not do is grow. Four things explain a balance that will not move: what entered the account, what was expected to clear it, whether the settlement timing is different from what was assumed, and whether something has been duplicated, omitted or misallocated.
The pattern that leaves one bank line
The pattern that holds up is a clearing account per rail, and it is the pattern the allied health canonical template encodes. In that template the fund benefit settles through 104 HICAPS clearing, card and online takings through 107 online payments clearing, and the processing cost lands in 604 merchant and claiming fees with GST on expenses. Every clearing account is bank type and BAS excluded, so a transfer through one does not touch the sales figures on the activity statement.
| Payment recorded in Halaxy | Clearing account | What happens to the fee |
|---|---|---|
| Scheme claim lodged through HICAPS Digital | The funder's own rail: 100 Medicare clearing, 101 DVA clearing, 102 NDIA clearing, 108 WorkCover clearing or 109 insurer clearing | No fee on the schemes HICAPS lists as free; 1.45 percent for the Transport Accident Commission and 10c an invoice for Medicare and veterans affairs, to 604 merchant and claiming fees |
| Fund benefit taken on a HICAPS terminal | 104 HICAPS clearing | HICAPS charges no fee to process a health fund or Medicare Easyclaim transaction on the terminal |
| Card payment taken in Halaxy | 107 Online payments clearing | 1.5 to 1.9 percent plus 75c to 1 dollar on the Silver and Bronze bands, to 604 merchant and claiming fees |
| Card payment on a bank merchant terminal outside the claiming channel | 106 EFTPOS clearing | Billed monthly to 604 merchant and claiming fees rather than netted from the settlement |
| Medicare bulk bill rebate | 100 Medicare clearing | The template's Medicare deposit carries no fee component |
- Receipt each invoice into its rail's clearing account, dated when the funder approved or paid it, with the claim or invoice reference on the payment.
- Match the bank credit as one movement out of that clearing account, splitting the fee onto its own expense line so the gross still clears.
- Read the clearing balance as the control: it is the money recognised but not yet banked, and it should fall back to nil after each settlement.
- Treat an aged balance as a claim that was paid and not matched, or matched and not paid, and chase it as one or the other.
What could not be confirmed
Halaxy's Xero articles were read in full for this page. Four things they do not settle are left standing rather than filled in, because each one changes what a practice has to do at the bank line.
- Whether Halaxy can write to Xero tracking categories. The Xero articles do not mention them, so this is a silence rather than a stated gap.
- Whether the HICAPS Digital fee is netted out of the settlement or billed separately, which decides whether the deposit arrives gross or net.
- Whether a day of fund benefits arrives as one deposit or one per fund, which decides how many clearing accounts a practice needs.
- What the accounting connection costs, which the pricing page does not name.
Where Ledger Map fits, and where it does not yet
Ledger Map holds one standing map for the practice, approved before anything posts. A line resolves to its account and tax rate through that map, a settlement is posted as one balanced document set per deposit so the bank feed is left with one exact match, and anything the map cannot resolve becomes a question with the options laid out rather than a silent posting. The account and the tax rate come from the canonical template the practice starts from, not from a treatment Ledger Map chose. You can read how the map works before deciding whether the pattern suits your file.
Halaxy is not connected in version one. Zanda and Stripe are the first two connectors, so a Halaxy practice takes the pattern from this page and applies it by hand for now. The clearing accounts, the fee treatment and the reference rule are the same work either way, which is the point of writing them down. The rest of the systems sit on every practice system.
Questions
Does the Halaxy Xero sync work both ways?
One way by default: records created in Halaxy appear in Xero, and records created in Xero do not appear in Halaxy. Two way syncing is a checkbox in the Xero sync preferences, and Halaxy limits it to invoice payments. With it on, a payment added or assigned in Xero updates the Halaxy invoice, and that payment can only be edited from Xero.
Why have my synced payments been counted as income twice?
Halaxy's answer is that the payment synced from Halaxy as income, and the same money was then coded as income again off the bank feed, which Halaxy cannot see. Its fix is a clearing account, with payments synced to a chart of accounts that is not the revenue account. A second cause is a rebate or scheduled payment that already records itself in Halaxy being marked paid in Xero as well.
Why does my Halaxy clearing account still hold a balance?
A balance during a funder's lag is correct: the claim is approved and the bank has not delivered it. A balance that grows is not. Check what entered the account, what was expected to clear it, whether the settlement timing differs from what was assumed, and whether a payment has been duplicated, omitted or coded to the wrong rail.
Where does the merchant fee go when a Halaxy payment reaches Xero?
Onto its own expense line, not into revenue and not into a rounding difference on the deposit. In the allied health canonical template that line is 604 merchant and claiming fees with GST on expenses, so the gross amount still clears the rail's clearing account and the fee is claimable where the practice is registered.
Does Halaxy charge for the Xero integration?
The pricing page does not name the accounting integration. It states that the platform is free, that credits cost A$0.15 to A$0.22 including GST, and that subscription features start at 25 credits a month. The cost of taking a patient payment inside Halaxy is published separately, at 1.5 to 1.9 percent per transaction plus a 75c to 1 dollar fee on the Silver and Bronze bands.
Read next
- FundersHICAPS settlements in Xero
- FundersPrivate patients: card, EFTPOS and Stripe
- FundersHow Medicare bulk bill payments land in Xero
- Practice systemsSplose Xero integration and the NDIS lump sum
- Practice systemsCliniko Xero integration: what syncs, what does not
- FundersTyro EFTPOS and HealthPoint settlements
- HubPractice systems
Sources
Open questions
- Halaxy's Xero articles do not mention tracking categories, so whether the sync can write to one is a silence in the documentation rather than a stated gap.
- Whether the HICAPS Digital fee is netted from the settlement or billed separately is unverified, and it decides whether a fund deposit arrives gross or net of the claiming cost.
- Whether a day of fund benefits arrives as one deposit or one deposit per fund could not be confirmed from a primary source, which is the same open question the HICAPS funder page carries.
- The cost of the accounting connection itself is not published. The pricing page lists credits and subscription features without naming it.
- Halaxy publishes its payment processing rate for the Silver and Bronze bands. The pricing page does not define the bands or name a rate for any other band.
- A live result page for the target query could not be captured, so the answer landscape in the brief rests on a real time search tool's report rather than on a measured ranking.
- Halaxy Xero integration tips for smooth syncing
My Great Bookkeeper. Retrieved 2 Sep 2026. Source updated 1 Jan 2025.
secondary
- Guide to two-way syncing between Halaxy and Xero
Halaxy. Retrieved 4 Sep 2026. Source updated 20 Oct 2025.
primary
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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