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    Jenny Mather commented  · 

    This a response I recently received from Xero this may help people

    One method you could use for settlement discounts for multiple bills is:

    Set up an account for the settlement discount. If you'd like to keep them separate, you can set up multiple for each supplier that offers this.
    During reconciliation, use Find & Match to search for the bills.
    To account for the difference between subtotal and money spent, click Adjustments, select Bank fee and then allocate the difference to the settlement discount chart of account account created in point number 1. You could set an appropriate VAT rate for it at this time.
    Click Reconcile.

    The bills will be fully marked as paid and the discounts will show in reporting. Alternatively, you could also:

    Raise a credit note for the amount of the discount instead and apply this.
    Edit the bill and use the discount field to lessen the amount due on the bill.