How do I apply 'payment link' credit card payment to an open invoice?

Thank you so much, Rose-A! This solved my problem and I greatly appreciate your assistance. This was a bit of a frustrating experience and I'm glad I have this reply to fall back on in the future when I encounter this situation again. Big thanks!

I had a similar original issue, and while I was able to match the Sales Receipt to the invoice and apply the payment, it's still adding the income from the Sales Receipt on top of the invoice total.

Eg. My project invoice is for $5,000, I sent a payment link asking for $2,500. I matched & applied the $2,500 Sales Receipt and it shows correctly as a payment on the invoice. But the customer/project shows $7,500 in sales. How do I fix this?

I appreciate you for providing us with detailed information. I'm here to provide some ways to get around with your concern, wegerm.

All sales transactions will reflect on the Sales dashboard. This means, regardless of what type of account you've chosen, it'll add up on the Sales dashboard.

To give you the best solution to your question, this way, we can avoid double entry. You can delete the Sales receipt and match the payment deposit to invoice .you made to correct it.

To delete sales receipt, you can follow the steps below on how to do this:

1. Select Sales in the left-hand menu
2. Go to the All Sales tab,
3. Click on the Sales Receipt you wish to delete
4. At the bottom of the page click on More and select Delete
5. Select Yes to confirm

Here's how to match the payment deposit to an invoice 

1. Go to the Transaction menu, and then Banking.
2. In the For Review tab, select the payment.
3. Choose Find Match or Find other matches.
4. Locate and select the open invoice.
5. Press Save once done.

In addition, you'll want to categorize and match online bank transactions with what you've entered in QuickBooks Online.

Feel free to post a reply if you have additional details on your question above. I'll be around to help you out. Have a pleasant day!

And just to be sure, can I delete the Sales Receipt without refunding the actual payment? Basically, keep the money but delete/void the record of the "extra" sale?

I was able to balance everything as-is by making a Credit Memo and matching the Sales Receipt to the bank Deposit instead of the Invoice. 

But my main question is: what is the best practice for requesting project deposits in QBO? Payment Link is nice because it doesn't require the customer to edit the amount like in the Invoice Payment screen. But maybe there's a better way.

I'm glad to provide additional insights about requesting project deposits in QuickBooks Online (QBO), wegerm.

QBO recently released the new version of estimates and invoices for your customers to commit to your projects.

You can request a deposit from an estimate if you're using QuickBooks Payments and the new version of estimates. Then, QuickBooks automatically:

1. Marks the estimate as accepted.
2. Converts the estimate to an invoice.
3. Records the deposit as a partial payment on the new invoice. 

I'm adding this link in case you find this interesting for your business: Request and accept deposits on estimates in QuickBooks Online. It'll also help check if you're seeing the updated version of the estimate.

If your estimate isn't updated, don't worry, our Product Team is migrating all QuickBooks account by batch. Once you see the update on your company file, you can start using the new estimate.

For now, you can use the progress invoicing process for accepting partial payments on projects.

Leave a comment below if you need additional information about requesting project deposits. I'm always around to provide steps and related articles to help you with the process.