Pay bills in a pay run (using Xero's Pay Run feature)
You can pay bills related to your pay run, such as payroll tax, separately from your employee payments while using Xero’s Pay Run feature.
In the Accounts menu, select Pay Run.
Open the pay run you want to make payments from.
Under Other payments, click on the bill amount you want to pay. This opens the invoice for that bill.
Complete the fields under Make a payment.The amount can be all or part of the bill total.
Click Add Payment.
Once a pay is fully processed, the status of the payslips will change from Awaiting Payment to Paid. If only partly paid, they will remain as Awaiting Payment.
The status for the whole pay run will only change to Paid once all the bills and payslips within it have been paid in full.