Once you have set up your Xero account for use with Cliniko, this article will show you through getting connected! We strongly recommend you seek your accountant's or bookkeeper's input when setting up your Xero account and the connection with Cliniko.

Here's an outline of what this article will cover:


First things first

☝️ Note: Please do not connect your Cliniko account to Xero before setting up Xero.

Before being able to connect Cliniko to Xero, you'll need an active Xero account, and for best results you'll need to set up that account first for seamless use with Cliniko.

Please read through the Set up Xero for use with Cliniko guide before going any further in this guide, to see how to set up your chart of accounts in Xero, and how to link the optional bits and pieces in Cliniko after you are connected. Once done, return back here to continue and get connected!


About Xero

Xero is an accounting software system that helps you see your cash flow in real-time. It also has online accounting, banking, and payroll features.

You may have a few questions about the integration—let's go through them!

How do I subscribe to Xero?

You can sign up for Xero on their website.

Are there any additional costs?

As Xero is a completely separate software system, they will have their own pricing structure, and you will need to pay their fees to use their services. Their pricing can be seen here. There is no cost to connecting Xero to your Cliniko account.

What does connecting Cliniko to Xero do?

Once you've integrated with Xero, Cliniko will automatically push all invoices and allocated payments from Cliniko across to Xero. Past Cliniko invoices and allocated payments can be synchronised as well. You can then perform more accounting related functions on your financial data, such as reporting and reconciliation against your bank feed.

Invoices are pushed across to Xero as soon as they are created in Cliniko. Payments are only pushed across to Xero once they are allocated to invoices in Cliniko, so unallocated payments in Cliniko won't be seen in Xero. Credit allocations in Cliniko also will not appear in Xero. Let us know if you have any questions about this!


Connecting the integration in Cliniko

☝️ Note: Before starting this process, you will need to have an account with Xero. Head over to their website to sign up (they do have a free trial!). Please also ensure that your Xero account is set up and ready for use with Cliniko.

Once you have your Xero all all set up the way you need it, you can get started on the integration process!

In Cliniko, head to Settings, and then Integrations:

Under Integrate with Xero, press the Connect to Xero button:

You'll be prompted to log in to Xero:

You'll be prompted to allow Cliniko to access your Xero account's data. Click Allow access:

There will be a message stating that Xero is bringing you back to Cliniko—don't leave the page:

The page will refresh, and you will now see more information on a new page, called Edit your integration with Xero:

Select the default Xero sales account for invoice items

☝️ Note: This is very important! The integration will not work until you complete these steps to set your default accounts.

Select the appropriate Xero account from under the Default Xero sales account for invoice items:

☝️ Note: The account numbers shown are an example only. You can set up your Xero chart of accounts however you need to. The accounts you see in this list will be pulled from whatever is set up in your Xero account. Learn more about setting up Xero for use with Cliniko here.


Select the default Xero clearing account for payments

Select the appropriate Xero account from under the Default Xero account for payments:

Depending on your Xero setup, this may be your bank feed, or a clearing account you have created.

☝️ Note: The account numbers shown are an example only. You can set up your Xero chart of accounts however you need to. The accounts you see in this list will be pulled from whatever is set up in your Xero account. Learn more about setting up Xero for use with Cliniko here.



Select the default Xero tax rate for tax exempt revenue

Select the appropriate Xero tax rate from under the Default Xero tax rate for tax exempt revenue:


Save your settings

Now the Integrate with Xero section should look something like this (remember the account numbers shown are an example only):

You've chosen your default accounts, and now you need to save the settings. Click the Save integration settings button, and you will be connected! Invoices created from this point onward will be pushed to Xero automatically, and so will payments allocated to those invoices.


Synchronising from a previous date

If you've already been using Cliniko for a while and are just now integrating with Xero, you can send all your old invoices and payments over to Xero quite easily! You may require only data from a particular date pushed across, such as July 1st.

In the Integrate with Xero section, click the link that says Synchronise from previous date:

Use the calendar to navigate back to the required date. Here, we've selected to sync from July 2022:

Click the Synchronise previous information to Xero button:

You'll then see a message indicating that Cliniko is currently preparing to batch sync your invoices and payments to Xero:

There are a couple of things to keep in mind with this!

  • It does not happen immediately. The batch sync process is a background task, meaning it is not high priority, and will run faster when Xero is not busy with other tasks. Invoices will generally make their way into Xero quicker, but payments will take a bit longer. Xero's API (the secure channel that is used for Cliniko to talk to Xero behind the scenes) only allows for one payment to be sent across each minute. This means that it you have a lot of older payments, they could take a few hours (or even days) to materialise in Xero.

  • It does not happen in any particular order. If you have invoices and payments numbered 1 through 5,000, number 2,591 might be the first one to hit Xero, and number 1 might be the very last! There's no way to tell which ones might be synched over to Xero first, but rest assured, they will all make it!

  • No data is duplicated in Xero. Only invoices and payments from the selected date that have not already been pushed across will be synchronised to Xero.

  • You can still create new invoices and payments in Cliniko while this batch sync is working. The batch sync is a background process, so it won't affect any work you're doing in Cliniko while it happens, and new invoices and allocated payments will be pushed across as normal.

  • Please keep in mind that payments made using account credit in Cliniko are not accepted by Xero. The invoices will sync over from Cliniko, but they will remain as open invoices in Xero (even though they would be closed in Cliniko). You will need to manually record the payment against that invoice in Xero if it was paid using account credit in Cliniko.


Viewing synchronised invoices

Are you wondering which invoices have been synced over? Click the View synchronised invoices link:

And you can see a list of all your invoices, as well as the status:

☝️ Note: If an invoice is marked as "Failed", there will be a message about why this is. Check out some of the common reasons as to why an invoice would fail to sync with Xero, or send us a message and we can help!


Specific settings

Now that Cliniko and Xero are connected, invoices and payments will automatically be synced over from Cliniko to Xero!

Remember that while you have the default accounts set up (as we outlined above), you can override this by setting up individual accounts in Xero and have Cliniko send each billable item, payment type, or product to a specific account. This is completely optional. Refer back to this guide for those details.


Please contact your accountant if you need any specific advice about your business, but let us know if you need any help with the setup. We are easiest reached from within Cliniko by clicking Help on the blue sidebar, and clicking Chat with us.

Once set up and your invoices and payment begin flowing across to Xero, you can begin reconciling. Reconciling can be tricky business, but with Cliniko and Xero, we make things easy. Follow this link to find out how you can use your set up to reconcile easily.

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