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Accept bank payments in QuickBooks Online

SOLVEDby QuickBooks163Updated November 20, 2023

Bank payments make it easy to accept large payments and stay organized. Unlike e-transfers, bank payments have no dollar limit per transaction, so customers can pay high-value invoices in a single payment. Also, we’ll automatically record and reconcile it for you, keeping your books accurate and organized.

With bank payments, you get:

  • A simple and secure way for customers to pay right from their invoice
  • A low 1% fee per transaction, capped at $100 per transaction
  • Automatically balanced books. We categorize each processed payment on your chart of accounts for you
  • No transaction limits

Note: Before you can accept bank payments, you first must be approved to accept credit card payments in Quickbooks.

In this article, you'll learn:

Apply to use bank payments

You'll need a QuickBooks Payments (Merchant Services) account attached to a QuickBooks Online account to process bank payments.

Payments-enrolled customers can see the option to enroll in bank payments in the English language product in two ways:

  • By navigating to the gear icon, selecting Account and Settings, then selecting Payments.
  • When creating an invoice.

Once you select the set up option, the bank payments application page opens in your web browser.

Follow the application flow including acceptance of Policy agreements. Once the Set up bank payments window displays, select the existing Deposit account listed or change your preferred bank account to manage transactions.


  • You must be the principal owner in order to apply.
  • You can only have one bank account to which your deposits are sent. Changing the account replaces your existing bank account for all payments, and the selected account will be used for all bank and credit card payments deposits.
  • The account must be transactional. This means QuickBooks can put money in and take fees out when needed without limitations.
  • The bank account must be based in Canada. You cannot put payments into foreign or out-of-country based bank accounts.
  1. Select Get set up to proceed. The Connect to your institution window displays.
  2. Select your banking provider from the available options.
  3. Enter your bank sign-in details when prompted.
  4. Select Continue. You are returned to QuickBooks to continue the bank payments setup process, and provided with a success notification in the window.
  5. Review and consent to the policy agreements.
  6. Select Get set up. A QuickBooks credential authentication message displays.
  7. Select your confirmation method and proceed. The processing window displays. You will be notified of your application status within 1-2 business days via email.
  8. Select the Payments tab.
  9. Review the Bank payments section to review the status of the approval process. The status of the approval displays a SETUP PENDING status.

If additional information is required in order to approve your request, you will receive an email notification requesting additional information or documentation that may be required.

Once enrollment is complete, bank payments will be added to the Payment Methods field and you can begin using bank payments to receive payments.

Send bank payment requests when creating an invoice

When you create an invoice, you will now have the ability to select the types of payments you’ll accept.

  1. Review the Bank payments box to activate the bank payments option when creating the invoice. You can offer multiple payment options an your customers will be able to pay the invoice using one of the options offered.
  2. Select the Save and send button. The Send email window displays the draft content of the invoice.
  3. Confirm that the draft content is accurate and complete.
  4. Select the Send and close button. A confirmation message displays, confirming that the invoice was successfully sent.

Your customer receives the invoice in their email inbox, and you are returned to the QuickBooks dashboard.

Once your customer makes their payment using bank payments, the funds will be in your bank account in 3-4 business days.

  1. Select Sales.
  2. Select the Deposits tab.

The deposit is reflected in your QuickBooks account.

What is nanopay?

While enrolling for bank payments, you will notice references to nanopay. nanopay is Intuit’s trusted partner that processes bank-to-bank transfers. Transfers are done securely within 3-4 business days with no transaction limits.

Bank payments transactions and fees associated with Bank transfers will reflect in your bank account as INTUIT NANOPAY.

Overview of the nanopay payer experience

  1. Your customer receives an invoice from you, the merchant, via email.
  2. In the invoice, your customer selects the Review and Pay link embedded in the email.
  3. A new tab opens where the user selects Pay with business bank account or Pay with personal bank account.
  4. They then log in to their online banking account to make a payment, where:
    1. Your customer can select the financial institution where the payment will be made from.
    2. They enter their online banking username and password to log into the bank portal to select the bank account.
  5. If the payer faces any technical difficulties during the process, they can select Use void cheque details to pay by providing their institution, branch, and account number.

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