I have a payment for an old invoice that is showing as a beginning balance in our A/R account. It is also showing on our A/R report as an item that is over 90 days old.

I'd like to share with you a method to clear your ledger and A/R report (Accounts Receivable) in QuickBooks Online (QBO), @gndirkes.

In QBO, you'll need to manually record the payment received since QuickBooks doesn’t automatically recognize when you receive payments. 

If the payment shows as a beginning balance in your A/R account, it indicates that it wasn't linked to the corresponding invoice. To clear both the ledger and A/R balance, ensure to link the payment to the respective invoice. Follow the steps below how:

1. Click the +New button
2. Select Receive Payment.
3. Enter the name of the customer or select Find by invoice no. and enter the invoice number.
4. Fill in the the details. 
5. Under Outstanding Transactions select the invoice to which the payment applies.
6. Click Save and Close.

You can run an A/R aging summary report as this gives an overview of the outstanding balances of your customer's payments and how long they're past due. 

Additionally, If you want to merge multiple transactions into a single record, check out this article: Record and make bank deposits in QuickBooks Online.

We are just around the corner in case you need further assistance with your reports. Have a great day!