We have paid a vendor but the bill shows unpaid. How do we clear this?

You can delete and then recreate the bill and bill payment, @sima3.

I've got steps on how to do this in QuickBooks Online (QBO).

First, you'll need to delete the bill that shows as unpaid. Let me guide you how:

1. Go to the Expenses menu at the left pane, and then choose the Vendors tab.
   
   
2. Find the vendor name associated with the bill, and then select the Transaction List tab.
   
   
3. Click the More button, and then tap the Delete option.
4. Hit Yes to confirm the action made.
   
   

Once done, recreate the bill and then re-apply the payments made.

If the same thing happens,  log in to your account using a private window. This can help us determine if it's a browser-related issue due to stored cache. You can use the following shortcut keys to access one:

• Ctrl+ Shift + N for Google Chrome .
• Ctrl + Shift + P for Mozilla Firefox  and Microsoft Edge .
• Command + Shift + N for Safari .

If it works, clear your browser's cache to remove the piled up files that cause unusual QBO responses. Then, go back to your regular browser and perform the task again. However, use another supported browser if you got the same result.

Also, the good thing is, you can run some bill reports to monitor all the payments made. Simply go to the Reports menu, and then refer to the What you owe section. These are the following:

• Bill Payment List report shows all the bills paid and the accounts used.
• Bills and Applied Payments report highlights all the payments you’ve made and the bills that go with them.
• Unpaid Bills report shows your unpaid bills, with due dates and days past due.
  
  

You can customize your reports to personalize them. Simply click the Customize button, and then choose the filters and info you want. 

You may also memorize them to save their customization settings for easy access. Browse this resource for the detailed instructions: Memorize reports.

Please let me know in the comment section if you have more QuickBooks concerns so that I can assist you further. Take care and have a fantastic day.