It's certainly not the experience we want you to have, Andrew. Let's troubleshoot this behaviour so your customers can receive their invoices accordingly.
The main reason that emails from QuickBooks Online or the 'do_not_reply' address goes to the spam folder is that your customers' email domains block @intuit.com. When the customers receive their invoices in their spam folder, they can select This is not spam or Not Junk.
Additionally, you may inform them to send a sample email to do_not_reply@intuit.com or add quickbooks@notification.intuit.com to recognise the @intuit domain as a trusted site.
If the same thing happens, they can consult with an IT expert to help add the QuickBooks Online mail server hostnames and IP addresses to their outgoing mail servers allow list so that QuickBooks emails that aren't marked as spam mistakenly.
For more troubleshooting steps, check out the resources from this article: 3 solutions for you when customers aren't receiving your emails.
On the other hand, I'm adding this material to know more about the invoicing feature in QuickBooks Self-Employed (QBSE): Create invoices in QuickBooks Self-Employed.
Please let me know in the comment section below if you have follow-up questions about your invoices and email entries. I'm just a few clicks away to help you again. Have a good one!
