This issue usually occurs when the payment for a Shopify sale is not properly linked and applied to the matching invoice in QuickBooks Online (QBO), asad8.

Although the connector shows the sales as "Paid," the QBO invoice's status is determined by whether a separate payment transaction has been specifically applied to it. Ensure that the payment for each sale is applied to its corresponding invoice in the program. We need to find the invoice and payment by following the steps below:

1. Go to My apps and select Sales & Get Paid.
2. Click Sales transactions.
3. Find one of the invoices that is incorrectly showing as overdue and note the customer name.
4. Check if there is a corresponding Payment or Sales Receipt that the connector should have created, usually for the same date and amount. This payment may be sitting in an account like Undeposited Funds waiting to be applied.

Then, apply the payment to the invoice by following the steps and details in this article: Record invoice payments.

On the other hand, the permanent solution is to ensure your Shopify connector is set up to record the payment and apply it to the invoice automatically. The most likely point of failure is how the connector maps the sales transaction. To learn more about this one, check out this article: Shopify and QuickBooks Online integration guide. The article is for International regions; however, some concepts in the US region.

Revisit this post if you have more questions about managing your sales transactions or QuickBooks-related concerns.