My nonprofit missed a tax payment. The next quarter, we paid the current payment, the overdue payment, and necessary fees/late charges. How do I record accurately?

Welcome to the QuickBooks Community, faubionpta-. I'll be sharing details on how tax payments work in QuickBooks Online. Then, to ensure you'll be able to record an adjustment for your overdue payment so it will show as paid in QuickBooks.

When you received a tax credit, discount, or penalties, you can always adjust the sales tax you owe. Since you've paid both current and overdue payments, I recommend making sure that you make an adjustment from the old tax payment to ensure you're allowed to edit the amount for taxes. This way, you don't have issues when it’s time to file. To start with, you'll have to set up an Expenses account for sales tax adjustment.

Here's how:

1. Go to the Gear icon ⚙️ and select Chart of accounts.
2. Click the New button.
3. From the Account Type dropdown, select Expenses since you need to increase your sales tax due.
4. Choose the account’s Detail Type.
5. Name your adjustment account (for example, sales tax due increase).
6. Click Save and Close.

Once done, you can now create an adjustment. Please follow the steps below.

1. Go to the Taxes menu and choose Sales tax.
2. Enter the date range in the Due Date Start and Due Date End dropdowns. Then, select Refresh.
3. Find the tax period you need to adjust and select View return.
4. Choose Add an adjustment.
5. Select the reason for the adjustment from the Reason dropdown arrow.
6. Add an adjustment date.
7. Select the account for adjusting sales tax from the Account dropdown list.
8. Enter the adjustment amount. Then, click Add.

After that, I suggest going to the Banking page and using the Find Match tool. Then, turn on Suggested Matches to locate transactions for tax payment so the program appears the overdue payment as paid. Follow these steps: 

1. From the Banking menu, select Banking and go to the For review tab.
2. Click the entry and select Find match. If you can't find the match, click Find other matches.
3. Turn on the Suggested Matches button. Then, look for the match transactions and check their boxes. 
4. Click Save.

Lastly, you may refer to this article to view detailed steps on how you can reconcile your accounts to avoid discrepancies: Reconcile an account in QuickBooks Online.

Don't hesitate to tag my name in the comment section below if you have other concerns in recording your tax payments in QuickBooks. I'm always ready to help, faubionpta-. Have a good day!