Answer
Disconnecting removes a Xero organisation (tenant) from Lightning Payroll's connection list. The disconnect is processed through Xero's API, so Lightning Payroll will no longer be able to submit journals or bank transactions to that organisation. You can reconnect at any time by going through the Xero login and authorisation flow again.
In the Desktop App
- Go to the Pays screen and start a Xero export (the option to export the pay run journal to Xero accounting software).
- Complete the authentication step if prompted. On the Xero Review step, the currently connected organisations are listed in the tenant selector.
- Select the organisation you want to disconnect from the dropdown.
- Click Disconnect Tenant.
- A confirmation dialog will ask: "Are you sure you want to disconnect '[organisation name]' from Lightning Payroll?" Click Yes.
- If successful, a message confirms the organisation is no longer connected. If no organisations remain, the wizard closes automatically.
In the Online (Web/Mobile) App
- Go to the Pays screen and select Xero Export from the export menu.
- On the Review Pay Run Before Export screen, select the organisation you want to disconnect from the Select a Xero company/tenant to submit to dropdown.
- Click the Disconnect '[organisation name]' button.
- Lightning Payroll removes the connection. If that was the only connected organisation, the screen navigates back automatically. Otherwise, the tenant list refreshes.

If you want to reconnect to the same or a different Xero organisation in the future, click Add Another Company/Tenant Connection on the same review screen and follow the browser-based Xero login and authorisation prompts.
For more about the full Xero export process, see How Can I Send Data To Xero From Lightning Payroll?. If you use MYOB rather than Xero, see How Do I Disconnect Lightning Payroll From My MYOB Account?.