Payment Workflow in Halaxy: From Invoice to Xero Reconciliation
Creating the invoice is not the end of the financial workflow. The payment still needs to be received, identified, applied correctly and ultimately reconciled against what actually reached the bank.
A client pays. An insurer sends a remittance. HICAPS or another payment provider processes a transaction. A bank transfer arrives.
But receiving money and accounting for it correctly are not the same thing.
Halaxy, Xero and the bank need to tell a financial story that can be followed and explained.
Payment Starts With an Invoice
Before there can be a payment workflow, there needs to be something for that payment to settle.
The previous billing stage established:
- the service that was delivered
- the amount being charged
- the practitioner or service involved
- the client or organisation responsible for payment
- the invoice against which the payment will eventually be applied
Billing Creates the Amount Owing
Payment records how that amount owing was subsequently settled.
The Halaxy Payment Journey
A useful way to think about the payment workflow is:
The Order Matters
Reconciliation is not what sends the payment to Xero.
The relevant accounting information needs to exist in Xero first.
It can then be compared with the bank activity and reconciled.
Paid in Halaxy Does Not Mean Reconciled in Xero
These are two different events.
Payment Received
Money has actually been received by the practice or its payment provider.
Payment Applied
Halaxy records which invoice or balance that money relates to.
Reconciliation
Xero confirms that the accounting record can be matched to the actual bank activity.
Recording Explains the Payment. Reconciliation Tests the Accounting Record.
A payment can look correct inside Halaxy and still create a problem when it reaches Xero.
Likewise, a bank deposit can exist without proving which client, invoice or payer it belongs to.
1. The Invoice Exists in Halaxy
The service has been delivered and billed.
At this point, the invoice represents an amount the practice expects to receive.
Until payment is correctly applied, the invoice may continue to form part of the practice's outstanding receivables.
- Who owes the money?
- Which invoice is outstanding?
- How much is outstanding?
- Is the payer the client or a third party?
- Is supporting information required before payment can be followed up?
2. The Money Arrives
Payments can reach a practice in many different ways.
Card Payment
Payment may be taken at reception or through a payment provider.
HICAPS / Tyro
Claims and payment activity may involve a separate payment or settlement process.
Halaxy Online Payment
A client may pay through the practice's online payment workflow.
Bank Transfer
Money may arrive directly in the practice bank account.
Third-Party Payer
Insurers, plan managers, employers or other organisations may settle invoices.
Other Methods
Some practices may still receive cash, cheque or other forms of payment.
Different payment methods can create different timing, settlement and identification issues.
3. Identify What the Payment Is Actually Paying
Before a payment is applied, the practice needs to know what the money relates to.
Depending on the payment source, that may involve checking:
- remittance advice
- invoice references
- merchant settlement information
- bank deposit descriptions
- client payment confirmation
- payer or claim references
- the amount received against the amount outstanding
If You Cannot Identify the Payment, Do Not Guess
Applying money to the wrong invoice may make one account look paid while leaving the correct invoice outstanding.
It also creates a problem that may not become obvious until much later.
4. Record and Apply the Payment Correctly in Halaxy
Once the payment has been identified, it can be applied to the appropriate invoice or balance according to the practice's workflow.
This helps Halaxy show:
- which invoice has been paid
- how much remains outstanding
- the client's or payer's remaining balance
- the payment information that forms part of the financial workflow
Do Not Mark Expected Money as Received
An invoice should not be treated as paid merely because the practice expects payment to arrive.
If Halaxy shows money as received before the payment has actually occurred, the operational record, accounting record and bank activity can begin telling different stories.
The Payment Date Matters
The payment date used in the workflow should be based on the evidence relevant to how the payment was received and how the practice's accounting process is configured.
Depending on the payment method, evidence may include:
- the transaction date
- remittance advice
- merchant settlement information
- the date funds reached the practice
- other supporting payment records
Inconsistent dates can make later matching and reconciliation unnecessarily difficult.
5. Use Outstanding Invoices as a Control
An unpaid or outstanding invoice report is not simply a list of people to chase.
It is also a useful control over the payment workflow.
Genuinely Outstanding
The invoice has not yet been paid.
Paid but Not Applied
Money may have been received but not correctly linked to the invoice.
Needs Investigation
The status may not make sense and needs to be followed through the workflow.
A Report Is Only as Reliable as the Workflow Feeding It
A clean-looking report does not prove the underlying payment process is correct.
Payment application still needs to be accurate and consistent.
6. Overpayments and Credits Need to Remain Visible
Sometimes the amount received is greater than the invoice being settled.
Depending on the circumstances and the practice's process, the excess may ultimately need to be:
- refunded
- held as a credit
- applied against a future invoice where appropriate
- otherwise dealt with according to the underlying circumstances
The Excess Money Must Still Be Traceable
Paying the original invoice does not make the remaining money disappear.
The excess needs to remain visible until it is properly dealt with.
7. Then the Relevant Information Reaches Xero
This is the sequence that is often misunderstood.
The Payment Is Not Reconciled First and Then Sent to Xero
The relevant accounting information needs to exist in Xero before it can be matched against bank activity.
Reconciliation comes afterwards.
Where Halaxy and Xero are integrated, the exact way information appears can depend on the configuration, transaction type and workflow being used.
That is why the goal is not simply:
“Did something sync?”
The better question is:
“Did the right accounting information arrive in the right place in a form we can reconcile?”
🥕 Halaxy & Xero Integration8. Merchant Settlements Can Change What Reaches the Bank
This is one of the areas where payment workflows can become confusing.
The amount paid by individual clients does not always equal one identical deposit in the bank account.
Payments Can Be Bundled
Several client payments may be combined into one merchant settlement.
Fees May Be Deducted
A payment provider may deduct merchant fees before the net amount reaches the bank.
Timing Can Differ
The client may pay on one date while the settlement reaches the bank later.
$1,000 Paid Does Not Always Mean a $1,000 Bank Deposit
If payments are bundled, fees are netted or settlement timing differs, the bank deposit may not mirror the individual patient payments one-for-one.
That is why settlement information can be essential when working out what the bank deposit represents.
Merchant Fees Need Their Own Accounting Treatment
Merchant fees are not the same thing as the client payment.
They are a separate cost associated with receiving the payment.
How they are processed may depend on the payment provider and the bookkeeping configuration.
- the gross amount paid by clients
- the merchant fee deducted
- the net settlement reaching the bank
- the correct expense allocation
- the appropriate GST treatment where applicable
These amounts need to be understood rather than simply forcing the net bank deposit against an unrelated accounting figure.
9. Only Then Do We Reconcile in Xero
Once the accounting information exists in Xero and the corresponding bank activity is available, reconciliation can occur.
Reconciliation Is the Reality Check
Does the accounting record properly explain the money that actually moved through the bank?
But the bank alone cannot tell you:
- which patient was paying
- which invoice should have been settled
- whether a third party paid the correct account
- whether a merchant settlement contains several patient payments
- whether the transaction was allocated to the correct account
- whether GST treatment is appropriate
That information comes from the wider workflow.
10. If It Does Not Reconcile, Follow the Transaction Backwards
A reconciliation problem does not automatically mean the bank feed is wrong.
The problem may have begun several steps earlier.
- Was the correct invoice created?
- Was the payment actually received?
- Was it applied to the correct invoice?
- Was the payment date appropriate?
- Was a settlement bundled with other payments?
- Were merchant fees involved?
- Did the relevant information reach Xero?
- Is the Xero transaction sitting in the expected account?
- Are Halaxy and Xero now describing the same underlying activity?
Do Not Force the Reconciliation Just to Make the Screen Go Green
A reconciliation should confirm a financial story that makes sense.
It should not be used to hide an unexplained difference created earlier in the workflow.
Halaxy, Xero and the Bank Do Different Jobs
The three records do not need to look identical because they serve different purposes.
But they should agree where the financial story overlaps.
Halaxy
Helps explain the practice activity, invoice and payment relationship.
Xero
Holds the accounting record and financial classification of that activity.
Bank
Shows the money that actually moved through the bank account.
The Goal Is Not Three Identical Screens
The goal is a transaction path that can be followed, supported and reconciled.
Outstanding Invoices Still Matter After the Bank Reconciliation
Payment workflow is not only about money that has already arrived.
The practice also needs a reliable understanding of what remains unpaid.
- genuine unpaid invoices
- payments received but not applied
- third-party accounts awaiting remittance
- credits or overpayments
- old balances requiring investigation
This is particularly important where outstanding receivables form part of the financial position or financial reporting of the practice.
When the Halaxy Payment Workflow Goes Wrong
Open the problem that sounds most like yours.
The presence of money in the bank does not automatically tell Halaxy which invoice it belongs to.
Check whether the payment has been properly identified and applied to the correct invoice in the practice workflow.
Follow the transaction from Halaxy into Xero.
Check what synchronised, where it landed, the date, the account and whether the accounting result reflects the underlying payment.
🥕 Halaxy & Xero IntegrationThis can happen where a payment provider settles multiple transactions together.
The settlement information should help explain which individual payments make up the bank deposit and whether fees were deducted.
A clearing account carrying an unexplained balance usually needs investigation.
Look at what entered the account, what should have cleared it, whether settlement timing differs and whether transactions have been duplicated, omitted or misallocated.
The objective is not to force the account back to zero.
It is to understand why the balance exists.
Check whether merchant fees were deducted before settlement.
Also check whether the deposit represents several payments, only part of a settlement or a different settlement period.
A completed bank reconciliation does not automatically prove that every transaction was allocated, dated, taxed or applied correctly.
If the figures still do not make sense, review the transaction path from the original invoice through payment, Xero and the bank.
🥕 Halaxy BookkeepingFollow the Complete Halaxy Workflow
Each card demonstrates its turn once. After that, use the 🐰 to turn it yourself. A 🥕 only appears inside a button that takes you to another page.
1. Workflow Design
Understand how the complete Halaxy practice workflow fits together.
Workflow Design
See how client activity, appointments, consultations, billing, payments and accounting connect.
2. Client Journey
Follow the client through the complete practice process.
Client Journey
Follow the client from first contact through service delivery, billing and payment.
3. Client Enquiries in Halaxy
Understand the client's need and identify the appropriate practitioner or service.
Client Enquiries
The practice establishes what the client needs and who is appropriately placed to help.
4. Appointments in Halaxy
Reserve the correct time with an appropriate practitioner.
Appointments
The appointment records what is scheduled to happen in the practice calendar.
5. Consultations in Halaxy
Move from what was scheduled to the service actually delivered.
Consultations
The consultation records what service actually occurred during the appointment.
6. Billing in Halaxy
Translate the service delivered into the invoice the practice expects to be paid.
Billing
Billing creates the financial amount owing before the payment workflow begins.
7. Payment Workflow in Halaxy
Identify the money, apply it correctly and follow the payment into the accounting workflow.
Payment Workflow
You are reading this guide now.
Payment explains how the invoice was actually settled.
Follow the relevant accounting information into Xero and reconcile it against bank activity.
8. Halaxy & Xero
Follow the financial information into accounting and bank reconciliation.
Halaxy & Xero
Halaxy helps explain what happened in the practice.
Xero records the accounting side of the transaction.
Why a Halaxy Bookkeeper Needs to Understand the Payment Workflow
Looking only at Xero can leave out the part of the story that happened inside the practice.
When something does not reconcile, we may need to understand:
- which invoice existed in Halaxy
- who was supposed to pay it
- what money was actually received
- how the payment was applied
- whether a merchant settlement was involved
- whether fees were deducted
- what information arrived in Xero
- what ultimately reached the bank
Sometimes the Xero Problem Started in Halaxy
And sometimes what looks like a Halaxy problem is actually a settlement, allocation or bookkeeping problem.
The transaction needs to be followed through the complete workflow before we decide where the problem began.
Payment Workflow in Halaxy — FAQs
Common questions about Halaxy payments, Xero and bank reconciliation.
A payment should be recorded according to the practice's actual payment workflow once the money has been received and the practice has enough information to identify what it relates to.
Do not treat expected money as received money.
Generally, an invoice should not be treated as paid simply because the practice expects payment.
The payment record should reflect what actually occurred.
Reconciliation comes afterwards.
The relevant accounting information needs to exist in Xero before it can be compared with bank activity and reconciled.
The difference may relate to payment application, timing, synchronisation, account allocation, merchant settlement or another part of the workflow.
The transaction needs to be followed from the original invoice through to Xero to determine where the difference began.
🥕 Halaxy & Xero IntegrationSeveral patient payments may have been bundled into one settlement, merchant fees may have been deducted, or settlement timing may differ from the transaction date.
Settlement information can help explain what makes up the bank deposit.
A continuing clearing-account balance may indicate timing differences, missing transactions, duplicated transactions, incorrect allocations or settlement activity that has not been properly cleared.
The balance should be investigated rather than simply written off to make the account zero.
Not necessarily.
Reconciliation confirms that accounting transactions have been matched against bank activity.
It does not by itself prove that every payment was applied to the correct patient, invoice, payer, revenue account or GST treatment.
We work across Halaxy, Xero and the bookkeeping workflow to help identify where financial information has stopped making sense.
That may include reviewing invoices, payments, settlement activity, clearing accounts and reconciliation issues.
🥕 Halaxy BookkeepingHalaxy Says One Thing. Xero Says Another. Follow the Money.
If a payment looks correct in Halaxy but stops making sense when it reaches Xero, forcing the reconciliation is not the answer.
The difference may have begun with the invoice, the payment application, the settlement, the sync or the accounting treatment.
We follow the transaction from the practice through Xero and into the bank to find where the financial story stopped matching.
🥕 Talk to a Halaxy Bookkeeper