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Hi Kassandra,
Yes, you can remove deposit listings from your GST calculation in QuickBooks Online (QBO) if they replicate your invoice listings. This is important to ensure that you do not double-count income when filing your GST.
You'll have to edit the deposit transaction and set the GST code to Out of scope so that it will not be reported in your BAS (Business Activity Statement).
You can run a Transactions by Tax Code report to easily edit your deposits.
For reference you can check this link about What to do when BAS amounts look incorrect.
Drop by again in the Community if you have further questions about BAS.