Applied invoice payments aren't displaying on P & L Report

Hi there, jreardon.

Let me share some information about how income and expense transactions show in the Profit and Loss report.

The Profit and Loss show your income, expenses, and net revenue and loss over a specific period of time. One of the possible reasons why the invoice payments aren't showing in the P&L is that maybe the service items are mapped for the Balance Sheet. You'll want to check if this is the case. 

1. Go to Lists > Items.
2. Double-click on the item you want to update.
3. Enter your changes in the Edit Item window.
4. Click OK.

Check this article for more details, Add, edit, and delete items.

Also, I'm adding a link to understand more about the reports in QBDT: Understand reports.

Please get back to me if you have additional questions. I'll be glad to help you more.

@jreardon 

Is it possible you're on accrual basis and the income is hitting the P&L when the invoice is issued and not when paid?  If it's showing on your balance sheet as part of net income, it must be on the P&L.  Net income on the P&L flows right over to net income on the balance sheet.