Why does Bill.com say bill has been paid, but it does not show in Payments Made?

Welcome to the Community @ppachon.

Let's figure it out by checking the Bills and Applied Payments report. This will show the bill and its associated payment for a specific payee.

Here's how:

1. In QuickBooks Online, select the Search icon.
2. Type bills in the search field.
3. Choose Bills and Applied Payments.
   

If you're able to see the bill and the payment made, I'd suggest contacting bill.com so they can trace the transaction. And, verify why paid bills didn't appear in Payments Made.

You can contact them through these links:

• bill.com/contact-us/ (call)
• support@hq.bill.com (email)
• https://help.bill.com/hc/en-us (forum).

Also, you may need to recheck out the Using the Payment Tracker to track the correct status of your payments. 

I've added a reference on how to record payments for the bills created in QuickBooks: Enter and pay bills.

I'll be looking forward to your reply. Please know I'm always here to help you. Take care!