Good day, @adam2280. Let me guide you in achieving this.
You can issue a credit back to your customer outside QBSE. About recording it, you'll need to exclude the invoice in the Transactions tab so it won't affect your financial reports.
Excluding the transaction is essential since QuickBooks Self-Employed (QBSE) doesn't have a direct way to issue credit back to a paid invoice or any available refund and reimbursement category.
Here's how:
- Go to the Transactions tab.
- Find the transactions you'll be excluding and tick the box beside them.
- Select the Exclude button above.

- After that, click Apply.
Moreover, you also need to exclude if there's any refund transaction showing in your account to offset the amount you've received or have credited back to your customer.
You might want to ensure that you categorize all your transactions to correct accounts to avoid discrepancies in your tax payments. Check out this article: Schedule C and expense categories in QuickBooks Solopreneur and QuickBooks Self-Employed.
Feel free to return here if you have more questions about invoice credit.