Happy to assist and see what options are available today but we would need more information on if this discount is being applied to sales or purchases transaction? Or are you referring to a discount given to you by the ATO, such as a refund on your last BAS lodgement? Hope to hear back soon with some of the finer details to assist.
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In order to advise how to record this we need to understand exactly what the discount was for and how you are trying to apply it. For example, did you lodge a BAS showing as owing a certain amount and the ATO has determined you only need to pay a certain amount of that? If so, are you needing to know how to record the 'part payment' of the BAS in QBO and then record the difference that will still show as owed?
As mentioned please feel free to reply with more details so we can best determine how to assist, or contact our friendly support team here who can go through the situation with you and offer more information. You may also wish to speak to your accountant for advice.
The tax discount is exactly as you describe it: total BAS is shown to be owing a certain amount, the ATO has given us a discount as COVID relief, we've paid the balance but the discount is still showing in my records as owed.
Just to double check if this in relation to COVID -19 Cash Boost for Employers you received? Or is a discount you've arranged desperately with the ATO? If it is in relation to the cash boost you can click here to see steps of bringing ATO Clearing Account back to zero and marking the BAS as 'paid'.
From a QuickBooks standpoint you can pay this owning amount to any offset account to and bring the owing amount to zero, payment notification will disappear, then you can journal the payment out. Whilst we cannot advise on which account to use as an offset or how to design the journal, it may be best you get in touch with a BookKeeper or Accountant for advise on what is best for your business.