Tracking direct payments from customers.

Hello, @macsme.

Thanks for posting here in the Community!

The possible reason why the customers' payments are showing twice on your Profit and Loss report is that you received the payment from the invoice and make a deposit associate with the Accounts Receivable (A/R) account.

If that's the case, your deposit will be an Unapplied Cash Payment Income, and the payment you received from the invoice will be a Sales of Product Income.

To link the deposit to the paid invoice, you'll want to delete the payment connected to the invoice first. Here's how to do it:

1. Find and open the paid invoice transaction.
2. Under the Payment Status section, click the payment made link.
3. Click the date link to open the Receive Payment page.
4. Select More at the bottom of the page.
5. Choose Delete, then Yes to confirm.

After that, you can now link the deposit to the invoice.

Here's how:

1. Click the + New Button, then select Receive Payment.
2. Select the customer from the drop-down.
3. In the Outstanding Transactions section, put a checkmark on the invoice.
4. In the Credits section, choose the created deposit.
5. Click Save and close.

You may also check out this article that tackles managing and linking deposits to an invoice in QuickBooks Online (QBO): How to link a deposit to an invoice.

Moving forward, you don't want to create a deposit to the invoice payment once it's already paid. This way, we can avoid unapplied cash payments in your QBO.

Reach out to me in the comment section below if you need additional assistance. I'll be around to help!

Hello,  Thank you for your response.   The problem I am having is not matching my manual deposits to invoices.   The problem started once we started using quickbook deposits.   We send our customers their invoices on line and if they choose to pay the invoice they then pay their invoices with a card etc at that time it matches with their invoice.   Then the deposit records in our profit and loss.  I have attached an ex.   Invoice  2102-002  Stella  $600.00  When payment is made by customer and recorded in checking our profit increases.

I can share some information about the profit and loss report in QuickBooks Online (QBO), @macsme.

When you deposit the payment of the invoice to the checking account that will increase your income in your Profit and Loss report. Receiving a payment from a customer affects your Accounts Receivable and your bank account. 

However, please take note of the accounting method that you set in your report. When you use the cash method in the report, it’ll only count as income or expenses once you process the payment received or sent. If you choose the accrual method, it’ll automatically count as an income or expense the time you sent the invoice or got the bill. Refer to this article for more information: Choose between cash and accrual accounting methods in reports.

In case some of your transactions are gone missing from the report, refer to the following article on how to resolve or find it: Why are my income and expense transactions missing from my Profit and Loss report?.

Let me know if you still have questions with your Profit and Loss report  by leaving a reply below. I'm always here to help. Keep safe and enjoy the rest of the day!