I want to turn off "auto-apply" for incoming payments. However, that option is not available on the "deposit settings" page. How can I turn it off?

I'm glad to see you here in the Community, hartholdingsinc.

You can turn off the automation feature QuickBooks Desktop through the Preferences.

Here's how:

1. Click Edit at the top menu bar and choose Preferences.
2. Go to the Payments tab in the left panel and hit Company Preferences.
3. Uncheck the Automatically apply payments option.
4. Click OK.
   

In case you want to know some "How do I" steps in QuickBooks Desktop, you can always visit our Help Articles page for reference.

Feel free to drop a reply below if you need additional assistance. I'll stick around to help you out.

That box was not checked.  

I appreciate you getting back to us, @hartholdingsinc.

Let's perform some troubleshooting steps so the payments won't auto-apply to your open invoices.

Since the Automatically apply payments option is turned off, let's run the Verify and Rebuild Utility tools to check if it's a data issue. It's a good start when it comes to fixing data-related issues.

To run the Verify Data utility:  

1. Click the File menu.
2. Select Utilities. 
3. Click Verify Data. 
4. If there are issues found, you’ll be prompted to Rebuild Now. 

Here’s how to run the Rebuild utility:  

1. Click the File menu. 
2. Select Utilities. 
3. Choose Rebuild Data. 
4. Click Ok on Rebuild has completed.

If the issue persists, you can read this article for additional troubleshooting steps: Fix data damage on your QuickBooks Desktop company file.

As always, feel free to visit our QuickBooks Community help website if you need tips and related articles in the future.

Please touch base with me here for all of your QuickBooks needs, I'm always happy to help. Have a good one.