How do I correct undeposited funds double counting deposits in bank register?

Let's get this corrected, MP11.

It's possible that you've added the deposits instead of matching it to the existing payments. This will create duplicate transactions in the bank register. 

You'll want to delete them. Here's how:

1. Click Lists, then choose Chart of Accounts.
2. Double-click the bank to open the register.
3. Look for a duplicate deposit, then double-click to open the transaction.
4. Press Ctrl + D on your keyboard.
5. You'll receive a message, "Are you sure you want to delete this transaction?", click OK.

I've got you an article for future reference: Add and match Bank Feed transactions.

I'll be here if you need further help from me. Have a great day! 

If you are using Sales Processes in QB, as Sales Receipts and Invoices, then a DEP is never Income to you. It is settlement or proof that the Sales Receipt funds were deposited or that the Invoice has a Payment to be applied.

All paid invoices need to have a Payment applied.

If you open a DEP and it shows as income, that is the manual duplicate and the error. Use the Payments Icon at the top. Select from here, what is In Transit and supposed to be listed Here. remove the entry of Income. This should end for the same total. Save and Close.

Replace all manual income deposits with the Right Transactions that are flowing from UF to the DEP worksheet. Do that until UF is 0, because you know you did all of your banking.

When our card sales come in from the bank its a combined amount of all the sales for the day. We generate Sales receipts for payments the account it defaults to is accounts receivable. Going forward do we need to default payments to undeposited funds or can we deposit directly to bank check register?  I was hoping not having to clean this up each month.

Thank you for your insight

Hello, MP11.

I'd be happy to help you with correcting your undeposited funds in QuickBooks Desktop.

Yes, you may choose either bank deposit or undeposited funds as the Deposit To. However, you'll need to do a bank deposit if you choose the undeposited funds as the default account.

Here's how:

1. Click Banking at the top menu, select Make Deposits.
2. In the Payments to Deposits window, select the payment/s that was deposited separately, then OK.
3. In the Make Deposits window, on a blank line, select the overstated income account from the From Account column drop-down.
4. Enter the negative amount in the Amount column. Make sure the Deposit subtotal is zero.
5. Select Save and close.

You can check out this recommended article: Understand how the Undeposited Funds account works.

This will get everything nice and organized in your QuickBooks Desktop account. Let me know if there's anything else you need. Have a good one.