Automatic payment allocation

Yes, there's a way to automatically apply payments to an invoice in QuickBooks Online (QBO), iamgavinjones.

Thank you for the screenshot. You don't need to create a rule for the deposit to automatically apply to the invoice.

QBO has an automation feature where you can automatically apply payments to an open invoice. This option can be turned on in the Account and Settings section.

Here's how:
 

1. Go to the Gear icon.
2. Choose Account and Settings.
3. Select Advanced on the left of the screen.
4. Click the Pencil icon in Automation.
5. Mark the Automatically apply credits box.
   
6. Click Save, then Done.

If these payments are creating an overpayment, I recommend the following article which contains steps for what to do: Apply A Credit From An Overpayment.

QuickBooks estimates and invoices are improving. Check out this link to learn about the latest update: See what’s new with estimates and invoices in QuickBooks Online. The workflow for these forms will look different depending on whether you have the old or the new version of estimates and invoices.
 

Let me know if you have other concerns aside from applying payments to invoices. I'll be right here to help you.

Hello, Gavin Jones. 

Thanks for your reply, and I appreciate the screenshot for clearer picture on what's going on. I'll give some details about the Automatically apply credits option, and how you can take care of those deposits and invoices. 

Just to clarify what the Automatically apply credits option will do, it only works on future invoices. For example, if the deposit was automatically categorised before the invoice was created, then the option will take effect (right after the invoice was created). 

The option won't work for existing invoices, so we're unable to automatically apply those deposits. Though, you'll want to continue manually linking and recording those payments. 

To make it easier, I'd recommend using the Receive payments option (go to the + New button, then select Receive payments). Just select your customer, then check the invoices and the deposits to link them together. 

Regarding the missing option, I double-checked the setting on my sample company, and it is still there. It looks like something is preventing it from appearing on your end.

If you want to use the option for future transactions, I'd recommend contacting our support. They can check on your account and investigate what's preventing the system from showing the option.

Here's how to reach them: 

1. Click the Help icon.
2. Select Talk to a human (or type it in the chat box).
3. When asked, enter "Automatically apply credits is missing " in the chat box. 
4. Choose I still need a human.
5. Click the Get help from a human link.
6. Select either the phone or chat option. 

If you need help with your bank account reconciliation in the future, feel free to use this article: Reconcile an account in QuickBooks Online.

I still encourage you to reply here if you have any other concerns with your customer transactions (or any other processes in QuickBooks). I'm always here to help.