How to Mark a Bill as Paid in QuickBooks Online

Once you've paid a supplier bill, you need to record the payment in QBO to clear the payable and reduce your bank balance. If you don't, the bill stays open in your AP aging report as if it's still unpaid.

If you are a Mesa Department Client, you can ignore this as your team will handle it for you.

What You'll Need

- Access to QuickBooks Online

- The bill already entered in QBO (see: How to Enter a Supplier Bill in QuickBooks Online)

- The payment date, amount, and which bank account or card you paid from

Normal Procedure

Option 1: Pay directly from the bill

1. Go to Expenses > Vendors and select the vendor.
2. Find the bill under Transaction List and click on it to open.
3. Click Make Payment (top right).
4. Confirm the Payment date, Payment method, and Bank/Credit account you're paying from.
5. Confirm the amount — if you're paying in full, it will default to the full balance.
6. Click Save and Close.

The bill is now marked as paid and the payment is recorded as a debit from your bank account.

Option 2: Use Pay Bills

If you have multiple bills to pay at once:

1. Go to + New > Pay Bills.
2. Select the Payment account (the bank account you're paying from).
3. Enter the Payment date.
4. Check the boxes next to the bills you're paying.
5. Confirm or adjust the amounts (you can make partial payments).
6. Click Save and Close.

Option 3: Match from the bank feed

If the payment has already come through your bank feed:

1. Go to Transactions > Bank transactions and find the payment in the For review tab.
2. Click Find match.
3. QBO will show open bills that match. Select the correct one.
4. Click Confirm to match and clear the transaction.

Abnormal Procedures

You paid part of a bill and the rest will come later.

In the payment screen, change the amount to what you actually paid. The bill stays partially open in your AP aging for the remaining balance. When you pay the rest, repeat the process.

You paid a bill but the wrong bank account was selected.

Void the payment and re-enter it with the correct account. Let your Mesa CPA bookkeeper know so they can confirm the correction didn't cause a reconciliation issue.

You paid a bill and it matched to the wrong vendor in the bank feed.

Undo the match from the bank transaction (click the transaction > Undo), then rematch it to the correct bill. Your bookkeeper can also fix this during reconciliation.

You paid a bill through a credit card, not a bank account.

In the Bank/Credit account field, select your business credit card. This reduces the credit card balance (liability) rather than your chequing account.

FAQ

If I match the bank feed to a bill, do I need to do anything else?

No — matching the bank feed transaction to a bill records the payment and clears the payable in one step. You don't need to also create a separate payment record.

Can I set up automatic bill payments in QBO?

QBO itself doesn't automate payments — that's done through your bank (pre-authorized debits or recurring transfers). What you can do is set up recurring bills in QBO so the liability is recorded automatically each period, even if the payment itself is still manual.

What if a supplier bill was entered and paid in a prior period, but I just found out it was wrong?

Don't go back and change prior period entries without talking to your Mesa CPA bookkeeper first. Prior period adjustments have tax implications and need to be handled carefully.

My AP aging still shows a bill as open after I paid it.

Refresh the report. If it's still showing, the payment may not have been applied to the correct bill — check whether the payment is sitting in the vendor's account unapplied. Your bookkeeper can resolve this.