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Hello there, MCooney.
There are several reasons why the transactions are showing in the VAT Exception report. I've listed some of the causes why these entries appear in the report:
Since the invoice for September was paid in November, it is the reason why it shows in the VAT Exception report.
To rectify this, it would be better to contact our QuickBooks Support specialist directly. They are the ones equipped with tools to further investigate why the transactions are showing both in the VAT Exception report and the Sales VAT report. Please consider getting in touch with them to help you fix it.
Additionally, visit our One Intuit Help Hub to access our troubleshooting guides, online resources, and FAQs specific to your QuickBooks products and needs. You can view this brief video to help you navigate the page seamlessly: https://intuit.me/OHHvideo.
Get back to the Community if you need other help. I'll be here to back you up in case you need one. Take care!