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Let me help and provide information about tracking shipping costs in QuickBooks Desktop (QBDT).
Firstly, you have to create two service items (not discount items) - the Shipping Cost and Free shipping items which will use a Shipping Cost income account. In the invoice, add the item you're selling and the shipping cost. Then create a credit memo to apply to that invoice and reduce the total invoice amount. In the credit memo, include the Free shipping item to offset the invoice amount. This way, the shipping cost account will show 0 and won't overstate or double the amount for the profit and loss since it is being used for offsetting the transactions.
To view the report, you need to run the Transaction Detail Report.
Here's how:
I'll add this article to help you customize the data, add or delete columns, add or remove information on the header/footer, and even personalize the font and style of the report: Customize reports in QuickBooks Desktop.
Please feel free to drop a comment below, if you have further concerns about tracking or other QBDT-related concerns. I will answer them in any possible way.