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This is not the kind of experience we want you to have, @Skeeg.
I can share some information about our categories in QuickBooks Self-Employed (QBSE).
To check about when transactions are classified as Allowable or Disallowable expenses, refer to this article: Allowable and disallowable expenses explained. You can also learn more on the HMRC website.
To further check why the same categories are giving inconsistent results, I suggest reaching out to our Customer Support team. They can check your account in a secure environment, verify the error and help you resolve them.
Here's how to reach them:
Check this article for more information about the different types of support we offer and their availability: Contact QuickBooks Self-Employed Support.
Then, refer to this article for more information about how your self-assessment report summarises all transactions that you have entered under each specific SA103F Categories: Transactions page versus Self-Assessment Summary page.
Stay in touch if you have any other concerns about our categories by leaving a comment below. I'm always glad to help in any way I can. Have a great rest of the day.