Payment Reconciliation Walkthrough Follow

The following article outlines the best practices associated with how to track and manage payments with Healthengine's Payments Reconciliation feature. This will help you reconcile your payments from within your Practice Management Software (PMS) as well. Please be aware that this Reconciliation page registers all transactions made via Healthengine, so will include payments from Medical Certificates, Scripts and Bookings.

To ensure you can see the Reconciliation page, make sure you have actioned the relevant permissions from within the Logins & Permissions section in Account.




Getting access to Payment Reconciliation in Practice Admin

In order to access the payment reconciliation dashboard, the account you are using needs the relevant permissions to view it. This is a level of protection available to your practice, to ensure that the privacy of your practices accounting is preserved. There is no limit to who can have access to this page, but it does need to be set up prior to viewing this page.


To do so, follow the below steps:

  1. Log into Practice Admin
  2. Go to Account < Logins & permissions
  3. Find the corresponding email addresses you want to grant access to
  4. Tick the box to turn the permission ON

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Reconciliation method 1 - Matching Payout Reports to your Bank Account

This method is best used if you want to check which individual payments constitute a payout from Stripe, and which payouts have been received into your bank account. This method will require you to have access to the relevant bank accounts linked to the Stripe accounts.

  • Access Practice Admin and navigate to Payments > Payment Reconciliation > Payouts to view all the payouts processed through Healthengine and Stripe. This page shows all the payouts, and the net amount that has been transferred into your bank account.

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  • Use the dashboard to select the payout you want to see the individual transactions for. You can use filters to help narrow down your selection if you wish to search for a particular date or receiving account.

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  • You can then check this total amount received and the account it was received into against the associated bank statement for the relevant account. If it is correct, you can then mark the payout as bank reconciled to acknowledge you have received this payout for your records.

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  • OPTIONAL: If you want more information on this payout, you can click "View" in the table next to the desired payout report to see a payment activity page with all the transactions that have been successfully deposited into your bank account. You'll see additional information such as the refund status of a payment, the type of transaction this was and the amount

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Reconciliation method 2 - Reconciling Payments to invoices in the PMS

This method is best used if you want to check which Healthengine payments have been paid, or which PMS patients have been marked as paid and corroborated with Healthengine. This method will require you to access your PMS.


Generating a PMS report

  • Within your Practice Management Software (PMS), generate a report displaying receipts within your specified date range that you wish to reconcile against. This report may be referred to as a 'Receipt Report' or a 'Banking Report' within your PMS.
  • Ensure the PMS report includes the payment method information and paid status. This is important so you can easily distinguish which payments have been processed via Healthengine and which have been done at your practice directly via other means.
  • Once created, calculate the total amount for all invoices paid via Healthengine (Typically done by filtering for only Healthengine payments) and count the total number of transactions present.
    • Note: It's recommended to use 'Direct Credit' (Best Practice) and 'Direct Deposit' (Medical Director and Zedmed) as payment methods for Healthengine and only for Healthengine. This helps segment which payments are processed via Healthengine's payments, and which you have obtained through other payment channels like EFTPOS


Generating a Healthengine Payment Activity reconciliation report

  • Access Practice Admin and navigate to Payments > Payment Reconciliation > Payment activity to view all transactions processed through Healthengine. 


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  • Using the filters in the top right, set the Charge Date in Healthengine to match the date range being reconciled in your PMS report.
    • If reconciling for individual specific practitioners, select the Practitioner checkbox and choose their name accordingly.
    • If looking to do bookings only, ensure the correct filter for 'Service Type' is selected (i.e ignore Medical Certificate charges since they aren't linked to a booking)
    • Note: If a practitioner doesn't have their own unique Stripe account, their billings will come into the practice Stripe account and associated bank account when paid out
    • Note: The 'Charge date' is the date the transaction was processed via Healthengine. Depending on how your practice manages prepayment and post payment, this might not match the patient booking date or appointment date.


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Dealing with transaction fees in Reconciliation

As part of processing a payment, Stripe and Healthengine take part of the transaction to pay for the service, and depending on how your practice has set this up, this might impact how you reconcile your accounting.

  • If your practice absorbs the transaction fees to the patient (i.e a $50 appointment is charged to the patient at $50, which is $49 practice fee and a $1 Stripe/Healthengine fee), use the Subtotal Charged value that appears
  • If your practice passes on the transaction fees to the patient (i.e a $50 appointment is charged to the patient at $51, which is $50 practice fee and a $1 Stripe/Healthengine fee), use the Subtotal net value that appears. This is the value of all the transactions charged to the patient MINUS the associated Healthengine and Stripe transaction fees, and should be the value your practice receives


Note: You can also generate a similar report from the Payout page as listed in the first method, and track the payout payment activities instead if that is easier for your practice.


Matching the Payment Reports together

  • Verify that the Subtotal net or Subtotal Charged dollar amount in Healthengine matches the total dollar figure in your PMS-generated report.

If the numbers do match

  • If the numbers do match, it means that all the PMS receipts have been correctly created and marked as paid at the correct rates
    • You can now reconcile the transactions by checking the checkbox to ensure they are marked as paid and received by Stripe
  • When completed, you have finished reconciling! Repeat these steps as needed for each reconciling period, and if you need to do this for individual practitioners

If the numbers don't match

  • If the numbers don't match, there could be a number of reasons for this:
    • An invoice wasn't created associated to a patient account
    • A receipt was marked incorrectly as paid or unpaid in your PMS when it shouldn't have been
    • A patient wasn't charged the same amount that Healthengine is reporting
  • To help narrow down the issue, count the number of transactions Healthengine reports as charging in the same charge period as your PMS report.
    • If the number of transactions are the same, it is likely an issue where the number Healthengine charged isn't the same as the Practice's report.
    • If the number of transactions isn't the same, its likely an issue where an invoice doesn't exist, or an invoice hasn't been marked correctly.
  • To solve this, you will need to go line by line through each payment from the Healthengine report and find the corresponding patient invoice in your PMS and see if it was marked correctly as paid, and with the same value.
    • You can do this via the Practice Admin interface, or you can download the CSV version

  • If you find a patient booking that doesn't have an invoice, or is marked incorrectly, you can create the invoice or update the status in your PMS, re-run the PMS report and check the Subtotal numbers again.
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