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Payment allocation for invoices

Have payments automatically apply to invoices the way you want them to! 💳

Joe avatar
Written by Joe
Updated over 2 months ago

You can automatically allocate payment to multiple outstanding invoices in Cliniko! When your patient or their insurer pays towards more than one invoice at once, Cliniko can help you to efficiently allocate payments based on the age of the invoice or what you're currently working on, while accommodating manual adjustments, too!

Only Administrators and Power receptionists can change invoice allocation settings. Learn more about the different user security roles here.


Setting up payment allocation

You can choose how automatic payment allocation works for your practice by adjusting the settings found in Settings, and then Invoices.

automatically allocate payments to

You have several options for how payments are allocated:

  • All invoices, starting with the oldest: Payments will be applied to the oldest outstanding invoices first.

  • All invoices, starting with the newest: Payments will be applied to the most recently-created invoices first.

  • Only the source invoice: Payments will be automatically applied only to the invoice currently being viewed when adding a payment. You can still manually allocate credit and payments to other invoices as needed.

  • No automatic allocation: No automatic allocation will occur; you will have full control over how payments are allocated.


Manual adjustments and auto-allocation

Cliniko’s auto-allocation process respects any manual adjustments you make. If you apply a portion of a payment to a specific invoice, the remaining amount will be automatically allocated according to your chosen setting. Similarly, if you manually apply available credit, only the remaining amount will be auto-allocated.

For example:

  • If you’re making a $500 payment and manually apply $100 to a particular invoice, only the remaining $400 will be automatically allocated to other invoices.

  • If you have $100 of available credit and manually apply $50 to an invoice, the remaining $50 of credit will be auto-allocated.

  • Manual changes to payment amounts or credit allocations will always be respected, and any outstanding amounts will be adjusted accordingly.


Allocations have been set up to offer flexibility and to make it easier to manage payments across multiple invoices. If you have any questions about this, please get in touch with our friendly support team. 👍

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