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Reconcile in Xero when using the Cliniko integration
Reconcile in Xero when using the Cliniko integration

Reconcile transactions in Xero.

Clinton Beeken avatar
Written by Clinton Beeken
Updated over 3 months ago

Now that everything is connected and set up as our set up guide recommends, you can start invoicing and documenting your payments in Cliniko! 

As the invoices are created and payments are allocated in Cliniko, they will be pushed across to the relevant accounts in Xero. As the information starts to populate, you will want to make sure that the money in your bank account is accurately reflected in your recorded invoices and payments. This is where reconciling occurs!

This article will cover:


Reconciling when Cliniko payments are syncing to the bank feed account

Please see Xero's article on reconciling your bank account here:
https://central.xero.com/s/article/Reconcile-your-bank-account as a starting point!

To help keep things running as smoothly as possible, we recommend always creating your invoices and entering payments in Cliniko first, and letting Cliniko sync them over to Xero for you—this means you won't need to do any double-handling (such as add the same invoices and payments into Xero!).

Here are some key things to consider when using Xero's reconciliation tool

When an invoice is marked as paid in Cliniko, that "paid" status also gets sent to Xero (so the invoice gets marked as paid in Xero, too).

If you then log into Xero and click "Reconcile", it can get a little confusing because Xero starts looking for unpaid invoices—however, the invoice has already been paid!

When one payment is applied to more than one invoice in Cliniko, that will appear as more than one payment in Xero, because that single payment is allocated to multiple invoices in Cliniko. It is the actual allocation of payment that is pushed across to Xero, not the one-off payment on its own.

So, let's say that a patient gave you $100 to pay off two $50 invoices:

  • This would land in your actual bank account as a single transaction of $100.

  • In Cliniko, it would be recorded as a single payment of $100, but it would be allocated across the two invoices.

  • In Xero, it would be shown as "two" payments (the allocation of that $100 to different invoices).

When reconciling in Xero, we recommend using the "Find & Match" function on the right-hand side of the screen, as in this example below:

"Find & Match" will help you find (and match!) a single bank transaction to multiple payments.

Xero has their own guide on using "Find & Match", which might be helpful as well!


Reconciling when payments are syncing to one or more clearing accounts

To start the reconciliation process, you will need a couple of tabs open. Here's what you'll need:

The clearing account report

  1. In Xero, head to Accounting Cash Summary.

  2. Find the relevant Clearing Account on the summary.

  3. Click on the monetary total for the month in question.

  4. Set your date range, and click "Update".

That will provide you with the total amount of payments pushed across from Cliniko for the date range selected.

The reconciliation page

  1. In Xero, head to Accounting Bank Accounts.

  2. Click on the Bank Account required.

  3. Click on the Reconcile tab.

That will bring you to the actual reconciliation page in Xero. This is where you will be reviewing your deposits.


Now, to reconcile

  1. Find the Deposit that you wish to reconcile.

  2. Confirm the deposit is the correct amount that you were expecting, by referring to your Clearing Account report.

  3. If that looks in order, click on the "Create" tab.

  4. Enter a name in the "Who" field for the transaction (e.g. EFTPOS Deposit).

  5. Select the "Acct" in question (in this case, the EFTPOS Clearing Account).

  6. Then hit "OK".

You have just reconciled your first deposit in Xero! Now, we'll explain what you just did.

When Cliniko pushes payments into your clearing account, we are creating "debits". This means that your clearing account is now increasing in value. The aim of reconciling to make sure that the money that you are receiving into your bank account is "zeroing out" the debits in that clearing account. By using the "create" function on the reconciliation page, you are now creating a "credit" in that clearing account. Thus, you are wiping off the debt that you have accumulated.

Essentially, Cliniko is saying "these are expected payments, clear this ledger when you receive these payments in your bank account" and the reconciling process is just you saying "I now have this money in my bank account, that debt can now be cleared."


Remember, before you can reconcile, you'll need to be sure that you've connected Cliniko to Xero, as well as set up all your appropriate accounts in Xero! First, you'll want to set up Xero for use with Cliniko. After that, you can integrate!

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