QuickBooks can track an invoice from start to finish by recording the customer’s payment and automatically depositing the money into the company’s bank account. However, if these processes occur in separate systems without a reliable connection between them, problems can quickly arise.
A QuickBooks payment integration connects the payment processing software to the accounting software used daily by the business or accounting staff. Using an integration can save time and allow for better visibility into the company’s accounts receivable.
Depending on the type of payment provider used by the company, such as QuickBooks Payments, a separate merchant account, or providers like NMI and Authorize.net, the integration will differ slightly from the other.
What Does a QuickBooks Payment Integration Do?
Beyond transferring the amount to be deposited into the business’s bank account, the integration should also transfer information about which customer made the payment, which invoice it applied to, and the processing fee.
Depending on the software applications involved, an integration may be able to facilitate the following functions:
- add payment options to invoices
- process credit card and ACH transactions
- mark invoices as paid
- create sales receipts
- synchronize refunds
- record processor fees
- group payments into deposits
- store tokenized payment methods
- support recurring billing
- match bank activity
- preserve transaction IDs
QuickBooks Online offers the closest integration with QuickBooks Payments. Intuit states that QuickBooks Online can only directly integrate with QuickBooks Payments merchant services. Any transactions from a third-party provider will require either a third-party software integration or manual synchronization of accounts between the merchant and accounting software packages.
For merchants who require a separate merchant account for various reasons, such as higher risk or more specialized products, the integration with accounting software will have to be performed manually.
3 Ways to Integrate Payment Processing With QuickBooks
| Integration Path | Best Fit | Main Advantage | Main Tradeoff |
|---|---|---|---|
| QuickBooks Payments | Eligible businesses wanting a native QuickBooks Online workflow | Payments, deposits and fees can update automatically | Standardized eligibility may not fit every high-risk business |
| Third-party payment connector | Merchants using NMI, Authorize.net or another approved account | Preserves merchant-account flexibility while reducing manual entry | Sync behavior and costs vary by application |
| Manual recording and reconciliation | Lower-volume businesses with simple payment activity | Works without an additional integration service | More staff time and greater risk of duplicate or unmatched records |
QuickBooks Payments
QuickBooks Payments is the best option for companies already using QuickBooks. This integration supports credit and debit cards, ACH bank transfers and other payment methods within the QuickBooks software. When correctly connected, QuickBooks can automate payments, recording and updating the accounting software file.
QuickBooks Online also records native payment deposits and fees automatically. Payments will enter the system, as will the settled batches and fee withdrawals into the bank.
This is the simplest option for an eligible merchant who wants to use one provider for invoicing, payments processing, and bookkeeping.
Third-Party Merchant Account Integration
A third-party integration between QuickBooks and a merchant account may be suitable for a high-risk or high-volume B2B company.
QuickBooks can automatically create a payment link or import transactions from the merchant account. However, invoices may only be marked as paid in the third-party program, not in QuickBooks.
Manual QuickBooks Recording
QuickBooks suggests that payments be manually recorded in the Undeposited Funds account. A deposit can then be created in the bank account, and the payment processor fee can be logged in as a negative value against the correct expense account in QuickBooks.
This method works best for merchants with limited sales and payments to manage. However, it can be challenging for merchants who process large batches of payments or have many payment channels.
How to Connect NMI or Authorize.net to QuickBooks
Payment Nerds works with NMI and Authorize.net for eligible merchant account configurations. Each company has a different method of connecting to QuickBooks.
NMI and Bill Connect
NMI’s QuickBooks solution is Bill Connect (by Biller Genie). Bill Connect connects to QuickBooks Online, QuickBooks Desktop and Xero to allow:
- Credit and ACH invoice payments
- recurring and bulk payments
- stored credentials
- branded electronic invoices
- automatic reconciliation
- automatic updates to paid invoices
- view customer payment history
NMI reports that companies using Bill Connect see a 40% reduction in overdue invoices, receive payments 15 days faster, and save 10-20 hours a week administratively. These reports have been compiled by the billers and are not guarantees of the results that will be received from implementing Bill Connect.
Merchants should understand how card-present transactions are handled by the system. With the gateway initiating these transactions, they will appear as sales receipts within QuickBooks. It is up to the merchant to associate these sales receipts with the appropriate invoice. If the invoice is marked as paid as a result of the sales receipt, that will result in the invoice being paid twice.
The older QuickBooks SyncPay plugin by NMI has reached the end of its support life on March 31, 2026. NMI now asks that merchants transition to Bill Connect instead of the older SyncPay plugin that is no longer being maintained.
Authorize.Net and Third-Party Connectors
Authorize.net does not offer a direct integration with QuickBooks. The merchant would have to use a third-party service such as Commerce Sync or another service listed in the Authorize.net partner directory.
Authorize.net does provide a legacy download report for older versions of QuickBooks Desktop. This report will allow the merchant to download the transactions and manually add them to their accounting software.
The following fields should be visible in the Authorize.net connector for QuickBooks:
- customer names
- invoice numbers
- invoice items
- sales and refunds
- processing fees
- deposit batches
- payment methods
- transaction references
- product or service details
- recurring payments
Providing an invoice number for the transaction originating from the gateway will allow for easier synchronization between Authorize.net and QuickBooks.
How to Set Up a QuickBooks Payment Integration Correctly
Before connecting to any payment provider, take time to document the way invoices, payments, fees and deposits are currently recorded in the books.
Follow these steps when setting up the integration:
- Confirm whether the business uses QuickBooks Online or Desktop
- Obtain final merchant-account and gateway approval
- Select the appropriate service (native or third-party)
- Back up the accounting records
- Map the fields between both programs
- Select the appropriate Undeposited Funds, deposit and fee accounts
- Determine the procedure for recording refunds and chargebacks
- Test one credit card and one ACH transaction
- Confirm that the appropriate invoice is marked as paid
- Confirm that the processor batch matches the bank deposit
- Ensure that processing fees are not duplicated in the accounting records
- Test refunds, recurring payments and card-present sales
- Restrict employee permissions
- Review the first batch of settlement statements with the bookkeeper
Do not test just the payment button. Confirming that a payment button authorizes a payment does not mean that the fee and deposit will show up in the accounting and bank records in the same way.
QuickBooks recommends resolving any open refunds for customers and reviewing the status of recurring payments before connecting an existing QuickBooks Payments account. Connecting accounts may impact user IDs, settings and existing GoPayment information in the accounting software.
How to Keep QuickBooks Payment Integration Secure
Do not enter card or bank account information directly into notes in QuickBooks or customer records. Store customer and provider information in a tokenized customer profile or provider-hosted payment page.
Provide access to accounting software based on each employee’s role. A bookkeeper may not have access to issuing refunds or viewing the settings for the payment gateway.
Businesses should also ensure that these systems can perform the following functions:
- Change deposit bank account
- Create and modify recurring payments
- Remove disconnected users
- Multifactor authentication
- Storage of payment credentials
- Provider responsibilities for PCI DSS controls
Common QuickBooks Integration Mistakes
Assuming that every merchant account will have a direct connection to QuickBooks Online is the most common mistake. Intuit only allows this integration for QuickBooks Payments; however, third-party software can help to sync data from the merchant accounting software to QuickBooks.
Other common mistakes include:
- Choosing an integration software before receiving merchant account approval
- Using an installation of NMI SyncPay that is not supported by QuickBooks
- Creating both a sales receipt and a paid invoice
- Replacing the sales journal record of net bank account deposits with gross sales
- Deducting processing fees twice when entering merchant account data
- Not including the invoice numbers on transactions
- Allowing customer data to create duplicate entries
- Neglecting to account for refunds and chargebacks
- Testing the integration with credit and debit cards but not ACH transactions
- Assuming that card-present sales will automatically update the open invoices
- Canceling the old merchant accounting provider before the new one is synced
- Giving every sales and billing employee access to the accounting software with administrative permissions
Even if the software integration claims to automatically reconcile sales and bank account deposits, manually completing the first few batches will help identify any issues with the software before months of entering sales and depositing funds into the business bank account.
QuickBooks Payment Integration FAQs
Q: What is a QuickBooks payment integration?
A: A QuickBooks payment integration connects the payments system to customer, invoice, and accounting records. It can receive payments directly into QuickBooks or receive transactions from an outside payment gateway.
Q: Can QuickBooks Online directly connect to any merchant account?
A: No. Intuit states that QuickBooks Online directly integrates with QuickBooks Payments. Any other merchant accounts will require either a third-party integration to connect the two systems or manually deposit the transactions into QuickBooks.
Q: Can NMI integrate with QuickBooks?
A: Yes. NMI integrates with QuickBooks Online and Desktop through Bill Connect, allowing customers to receive card and ACH invoice payments into QuickBooks. Some features are only available with specific merchant account configurations.
Q: Does NMI SyncPay still work?
A: NMI SyncPay for QuickBooks is no longer supported after March 31, 2026. The company recommends that businesses use Bill Connect instead. It is not advisable to construct a new integration around the SyncPay plugin.
Q: Does Authorize.net integrate directly with QuickBooks?
A: Authorize.net does not directly integrate with QuickBooks. However, they do recommend using third-party services such as Commerce Sync.
Q: Can QuickBooks process ACH payments?
A: QuickBooks Payments does allow eligible ACH bank payments. Additionally, third-party service integrations such as NMI Bill Connect also allow ACH payments through the merchant’s account.
Q: Will an integration automatically reconcile every deposit?
A: The answer is no. It depends on the third-party application integrating with QuickBooks and how the payments are taken in. Many card transactions and refunds will require manual reconciliation.
Q: Can a high-risk merchant use QuickBooks payment processing?
A: The business can use QuickBooks for accounting functions. However, high-risk merchants will need to use a separate high-risk merchant account for payments. Third-party payment software may be needed to synchronize these two accounts.
Q: Should merchants keep card details in QuickBooks?
A: Merchants should avoid storing the complete payment card details within QuickBooks. Instead, only tokens for these accounts or payment forms within a payment vault should be used.
Keep Your QuickBooks Payments and Accounting in Sync
Link each payment to the correct invoice, fee, and deposit. Payment integrations with QuickBooks directly offer the simplest connection between payment and accounting software. Other vendors like NMI, Authorize.net, and others may require third-party tools to connect these two platforms.
Choose a merchant account and then determine which payments will show up in QuickBooks. Ensure that the entire process is tested to avoid duplicate income and inaccurate reports in QuickBooks.
Sources
- Intuit. “Integration With Third-Party Merchant Services in QuickBooks.” Accessed August 2026.
- Intuit. “Connect QuickBooks Payments to QuickBooks Online.” Accessed August 2026.
- Intuit. “Record QuickBooks Payments Deposits and Fees.” Accessed August 2026.
- NMI. “Bill Connect Integration.” Accessed August 2026.
- NMI. “Bill Connect by Biller Genie.” Accessed August 2026.
- NMI. “QuickBooks SyncPay Installation and End-of-Life Notice.” Accessed August 2026.
- Authorize.net. “Does Authorize.net Work With QuickBooks?” Accessed August 2026.
