Xero Integration



FlexiTime will no longer integrate with Xero from 28 February 2021. If you'd like to continue sending payroll invoices to Xero, we recommend upgrading to PayHero. Please contact support if you need any further information.

Alternatively, refer to this article to see how you can continue to manually send payroll data to Xero.


FlexiTime integrates with Xero, an online accounting system designed for small businesses and their accountants.

By integrating FlexiTime with Xero you can:

  • automatically create draft accounts payable invoices in Xero for Payroll transactions
  • assign costs to Xero Tracking Categories. 

For more information about Xero, see the Xero website.


Set Up Xero Integration

First, you must authorise FlexiTime to access your Xero account information.

To authorise FlexiTime go to Setup > Company Settings > Connect and click the Authorise button beside Xero Access. 



This will open a Xero login window so make sure you have allowed pop-ups in your browser; you may be given a message at the top of the browser window asking if you want to allow pop-ups. Log into your Xero account as you would normally. You will then be asked which organisation to authorise FlexiTime to access.



Select your Xero organisation and click Authorise. After a few seconds the window will close and you will be returned to FlexiTime and given the message that your company settings have been saved.

You are now set up to transfer data between FlexiTime and Xero.

Once you have authorised your FlexiTime company to Xero, you can select whether you want to send Draft or Approved invoices to Xero.  We recommend using the Draft Invoice Status initially, as it means that invoices will still be sent even if you have not set all your Xero accounts in FlexiTime. 

You can also tick Consolidate Invoices if you would prefer to send a single invoice through to Xero for all employees in the pay run.

If at anytime you want to delink FlexiTime from Xero, just click Disconnect



If Xero loses your FlexiTime authorisation, the Authorise button will show on the Connect screen.


Set up Account Codes

If you have changed the default account codes in Xero's Chart of Accounts you will need to set these up in FlexiTime so that invoice lines are posted to the correct accounts. 

When a pay is finalised, FlexiTime will create accounts payable invoices in Xero. Each pay line can be applied to a separate Xero account in your Chart of Accounts. See this article for information on how to split your wages into different accounts for each employee, or by pay code.


Set Up Tracking Categories

(Optional) FlexiTime can send tracking categories through to Xero if you use them. Please see this article for more information. 


Payroll Invoices

FlexiTime will automatically create draft accounts payable invoices in Xero for the wages and PAYE payments when you finalise a pay.  

On the Pay History tab, select the Pay you wish to finalise and click edit. Finalised Pays will not have the Edit option, you can only View these.

Check the details and then click Finalise Pay. A warning box will be displayed - click Yes to finalise the Pay.



FlexiTime will also automatically send a Credit Note through to Xero if you reverse an employee out of a finalised pay run.

If you have already finalised a pay but wish to resend the payroll invoices to Xero for any reason, simply View the pay, click the Options dropdown and select Resend to Xero.



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  • Avatar
    Christina Vellasamy

    Step by Step explanations great. Thank you.