How To Pay Bills in QuickBooks Online: Step-by-Step Guide (2026)

Paying a bill in QuickBooks Online (QBO) can mean two different jobs. Sometimes you already paid the vendor from your bank's website, with a business credit card, or with a check you wrote by hand, and you only need to record that payment against the open bill. Other times, you want QuickBooks to send the money for you by ACH transfer or mailed check. QBO handles both, but each one starts from a different screen, and mixing them up is one of the most common reasons a bill ends up paid twice in the books.

In this guide, I walk you through both methods using the current QBO menus. I also cover autopay for recurring bills, partial payments, vendor credits, canceling a scheduled payment, and what QuickBooks Bill Pay charges per payment as of October 2026.

Why you can trust Fit Small Business

I have more than five years of hands-on experience using QuickBooks, including managing accounts payable, processing vendor bills, recording payments, and reconciling bank transactions for US-based businesses. As a QuickBooks Online ProAdvisor, I've handled full-cycle bookkeeping and worked with payment tools such as QuickBooks Bill Pay and Melio.

I've also dealt with duplicate payments, unapplied vendor credits, and other issues that can arise when bills and payments aren't recorded properly. This guide combines my practical bookkeeping experience with QuickBooks' current payment workflows to help you pay vendors correctly, avoid duplicate transactions, and keep your accounts payable records accurate.

JR Suralta

Certified QuickBooks Online ProAdvisor and Certified Xero Advisor

Before you pay bills in QuickBooks Online

Both methods in this guide apply a payment to a bill that already exists in QuickBooks. If you haven't entered the vendor's invoice yet, start with our tutorial on how to enter bills in QuickBooks Online. Bills you create with QuickBooks Bill Pay's AI bill creation may wait in the For Review tab until you save them, so check there if a bill seems to be missing.

You also need the account you pay from set up in QuickBooks. For Method 1, that can be any bank or credit card account in your chart of accounts. For Method 2, Intuit connects a bank account through micro-deposit verification, or you can pay from a QuickBooks Checking account.

Method 1: How to record a bill payment in QuickBooks Online

Use this method when the money already left your account, or will leave it, through a channel outside QuickBooks. Recording the payment closes the bill, reduces your accounts payable balance, and gives the bank feed something to match when the transaction downloads.

Step 1: Open the Pay Bills screen

Select + New (or + Create, depending on your view), then select Pay bills under Vendors. Intuit's help center also lists a dashboard shortcut: Expenses & Pay Bills, then Pay bills. The screen lists every open bill with its due date and open balance.

Step 2: Choose the payment account

From the Payment account dropdown, select the account the money came from. Pick your checking account for a bank transfer or check, or pick a credit card account if you charged the bill to a business card. When you choose a checking or savings account, you can also enter a starting check number. If you plan to print the checks from QuickBooks, follow our guide on how to write and print checks in QuickBooks Online.

Step 3: Enter the payment date

Enter the date you made the payment. For a bank transfer, use the payment date shown in your records. If you paid by check, use the date the check was issued, not the date it cleared your bank. This helps keep your bill payment records accurate and makes it easier to identify outstanding checks during bank reconciliation.

Step 4: Select the bills and confirm the amounts

Select the checkbox next to each bill you paid. QuickBooks fills in the full open balance, and you can type a lower amount in the Payment column to record a partial payment. The bill stays open with the remaining balance until you pay the rest. If you have a credit from that vendor, apply it in the Credit applied column so the payment reflects the net amount you owe.

Step 5: Save the payment

Select Save (or Save and close). QuickBooks creates a bill payment transaction for each vendor, marks the bills paid, and removes them from the open bills list.

Step 6: Match the payment in your bank feed

When the payment downloads from your bank or credit card, go to Bank transactions and open it in the For Review tab. QuickBooks usually suggests the bill payment you recorded. Select Match to link the two records. If a single bank withdrawal covered several bills, use Find match and select each related bill payment.

Method 2: How to pay bills online with QuickBooks Bill Pay

Use QuickBooks Bill Pay when you want QuickBooks to move the money. Intuit sends the payment by ACH or mails a check on your behalf, and the payment posts to your books automatically. Bill Pay Basic comes with your QBO subscription, and standard ACH payments cost nothing on every Bill Pay plan.

Step 1: Activate QuickBooks Bill Pay (first time only)

Go to Expenses, select Bills, then select Schedule payment. QuickBooks asks you to pick a plan (Basic, Premium, or Elite) and complete a short application. Intuit says the application takes under 10 minutes and that the business owner should complete it. Have this information ready:

• Business phone number, address, and Employer Identification Number (EIN), which should match IRS records
• The owner's date of birth, home address, and the last four digits of their Social Security number (Intuit may ask for all nine in some cases)
• The bank account you'll pay bills from
• The bank account or credit card for your subscription charges

Review your selections, select Finish setup, confirm your subscription payment method, and select Subscribe. Most applicants get an instant decision. If Intuit needs more verification, you'll get an email with a decision within three to five days after the review.

Step 2: Go to your unpaid bills

Go to All apps, then Expenses & Bills, then Bills, and open the Unpaid tab. If a bill you expect isn't listed, check the For Review tab.

Step 3: Select the bills to pay

Find the bill in the list, or use the batch checkbox to select several at once. Bill Pay Basic lets you select up to 20 bills at a time, while Premium and Elite raise the limit to 50.

Step 4: Select Schedule payment

For a single bill, select Schedule payment in the Action column. For several bills, select Schedule payment from the table header that appears after you check the boxes. QuickBooks may send an authentication code to the phone number of the person making the payment.

Step 5: Set the payment details

Fill in each field for every bill you're paying:

• Bank account: The account Intuit withdraws the money from.
• Withdrawal date: The date Intuit starts processing the payment. Delivery time counts from this date.
• Payment speed: Standard, or a faster option for a fee when your account is eligible.
• Amount: The full balance or a partial payment.
• Note: A message or reference, such as the invoice number, that the vendor sees in the email notification and on the check.

Step 6: Review and schedule the payment

Select Continue, review each payment, then select Schedule payment. You and the vendor both get an email confirmation, and you each get another one when the payment starts processing. Your vendor doesn't need a QuickBooks account to receive the money.

Step 7: Track the payment

Open the Bill payments page under Expenses & Bills to see the status of each payment. For checks, you can view and download an image of the cleared check by selecting View details, then View check. The image appears about five days after the check clears, and not every bank supports check images.

If you want to change which ledger account Bill Pay payments post to, open the Pay from dropdown, select Manage, choose the bank account, and map it to the right account in your chart of accounts.

How to set up autopay for recurring bills

Intuit built autopay for fixed monthly bills, such as rent or a software subscription. Here's how to turn it on:

1. Go to All apps, then Expenses & Bills, then Bills.
2. Select the Recurring tab.
3. Select Add bill, or find an existing recurring bill and select Turn autopay on.
4. Confirm the interval.
5. In the Pay from dropdown, select your bank account.
6. Select Add payment method, choose the payment type, and select Save.
7. Select Continue, then Save and Schedule Payments.

How to send an instant payment

When a vendor needs money right away, check whether Instant Payment is available for that bill. On the Schedule bill payment page, select Instant in the Payment speed column, choose the amount, review the processing fee QuickBooks displays, and select Schedule payments. Intuit charges 1% of the payment, with a $100 maximum fee and a $10 minimum payment, and availability depends on eligibility.

How to cancel or void a QuickBooks Bill Pay payment

You can cancel an ACH payment while it's in Scheduled or Processed status, up to 5 p.m. on the day it's set to reach the vendor. You can void a mailed check once it shows Shipped status. To cancel a payment:

1. Go to Expenses, then Bill payments.
2. Choose the payment and select View details.
3. Select Cancel this payment.

After you cancel or void the payment, you can schedule a new one to the same vendor. Intuit also automatically voids any Bill Pay check that the vendor doesn't cash within 90 calendar days.

QuickBooks Bill Pay fees, plans, and delivery times

Recording payments with Method 1 costs nothing beyond your QBO subscription, which starts at $38 per month. QuickBooks Bill Pay adds per-payment fees only for checks and faster delivery.

Delivery times can vary because of third-party delays or risk reviews, and business days exclude weekends and federal holidays.

The three Bill Pay plans share the same payment fees. What changes is the batch size, 1099 filing, and approval controls:

Intuit is currently advertising 50% off Premium and Elite for the first three months. For a full breakdown, read our QuickBooks Bill Pay review.

Common mistakes when paying bills in QuickBooks Online

Most bill payment problems I see in QBO files come from a handful of habits:

• Recording the same payment twice: A bill payment recorded with Method 1 and the matching bank download added as a new expense will double the cost. Match the bank transaction to the bill payment.
• Paying an entered bill with an expense or check transaction: The money goes out, but the bill stays open, so accounts payable looks higher than it is. Apply the payment to the bill through Pay Bills or Bill Pay.
• Using the wrong payment date: A date that doesn't match the bank statement makes reconciliation harder and can shift the expense into the wrong month on cash-basis reports.
• Scheduling ACH on the due date: Standard ACH takes 3 to 5 business days, so a payment scheduled on the due date arrives late unless you pay for faster delivery.
• Skipping the vendor credit: Paying the full bill when you have an unapplied credit overpays the vendor and leaves a credit sitting in their account.

If your bank balance and QuickBooks still don't agree after you pay bills, our guide on how to do a bank reconciliation walks through how to find the difference.