Invoice payment deposited into bank account not linked to my QBO account -- how to reconcile?

Welcome to the Community, mrweiner. 

I've got steps on how to handle this in QuickBooks Online. We'll have to create a bank deposit to link the invoice payment less the amount of the fee. Please note to refer to the bank statement when reconciling your account.

Here's how to make a bank deposit:

1. Select +New and choose Bank Deposit.
2. From the Account drop-down ▼, select the account you want to deposit the money into.
3. Select the box for each payment.
4. Select Save and close.

For more information, please refer to this article: Record and make Bank Deposits in QuickBooks Online

I've also added links about reconciliation in QBO:

• What's a reconciliation?
• Learn the reconcile workflow in QuickBooks
• Fix beginning balance issues during your first reconciliation in QuickBooks Online

Let me know if you need anything else. I'll be around to help.

@mrweiner 

I can easily write myself a check to the Corp from the Sole Prop but not sure how to reconcile this & handle the orphaned entries. I'd assume it's something with "match" but not sure exactly what to do.

Yep that is what you do, then do a manual recon of the account.  In the sole proprietor account you would make the deposit as equity investment, and the check would use equity drawing as the expense

In the corp account, use make deposits after you actually make the deposit in real life

@GlinetteCThank you for the info, but I'm unable to follow the steps as provided. When I'm on the Bank Account form, there are no payments listed for me to select.

EDIT: Sorry Rustler...looks like I replied to the wrong comment.

Thanks for keeping us updated and I've read the thread as well, mrweiner.

In QuickBooks Payments, we can set an account to where we'll deposit the payments of the invoice. It's possible that you've set it to default as Undeposited Funds. I'll show you how we can update and verify that:

1. Go to the Gear icon and click Account and Settings. 
2. Select the Payments menu. 
3. Click QuickBooks Payments and review and edit the account. 
4. Once done, click Save and then Done. 

We can also review an invoice payment that was deposited to the Undeposited Funds account. Just click Sales and select Invoices. Click the linked payment and review the account that's under the Deposit to field.

Then, we can go back to the Bank deposit page to see if the payments are now listed under the Select the payments included in this deposit section. 

You can also use these articles on how to manage your bank feeds: 

• Assign, categorize, edit, and add your downloaded banking transactions
• Categorize and match online bank transactions in QuickBooks Online

Feel free to get back to us if you need anything else. You take care always!

Thank you for the extra info. I actually sorted this all out a few minutes ago. The issue was that since the invoiced payment did deposit (just into the wrong bank account), the payment was already associated with an existing deposit.

I had to delete the existing deposit, as well as the auto-generated Bank Charge expense relating to the payment processing fee. Afterward I was able to create a new deposit, where the payment was now present since it was disassociated from the auto-generated deposit.