QuickBooks and Payment Gateway Integrations: Simplifying Transactions


Payment processing is a vital business function. It can help your company operate more efficiently, provide better customer service, and stay competitive. Effective payment processing also means you’ll be able to improve your cash flow and reduce the risk of fraud.

And if you’re using QuickBooks accounting software, integrating payment gateways can further streamline the process through a simple setup for secure transactions. 

In this blog, we’ll help you navigate the complexities of integrating payment gateways with QuickBooks, to make the most of your accounts receivable operations. 


Understanding Payment Gateway Integrations

A payment gateway is basically a middleman between your customer, business, and both your banks during an online transaction. After your customer initiates a card transaction, the software securely captures their payment details and sends them to the relevant parties for authorization, so that it can be processed. 

But how does it work? A payment gateway is known as front-end technology, because it functions on the user interface of your web pages or app. However, there are different kinds of gateways. 

Generally, they fall into two main categories:

  • Hosted payment gateways. These redirect your customer from your web page or app’s checkout page to a payment service provider’s site. Once the transaction is complete, the software redirects your customer back to your site. 
  • Non-hosted or on-site payment gateways. Here, your customers stay on your site or app during the payment process, as the payment gateway is integrated directly into your site.  

Each kind has its advantages and disadvantages. For example, hosted gateways tend to handle the security and payment processing, while non-hosted sites give you more control over the transaction, and provide a smoother customer experience. 

Benefits of integrating a payment gateway with QuickBooks

As mentioned above, integrated payment gateways give you more control over your transactions. In addition, they provide security for your financial information, as they must adhere to strict security protocols. And as an added bonus, they can help you attract and retain customers, even internationally.  

By integrating with QuickBooks, you get even more benefits, as all your transactions and documentation are recorded in a single place – your accounting software.  


For starters, having an integrated payment gateway can save you time and money, as this software automates your invoicing and financial records. That means you won’t have to dedicate time to tracking and reporting your sales transactions. This also means increased accuracy, as you won’t have potential calculation errors, redundant entries, or misplaced invoices. 

Together, this can assist your finance team with better forecasting, and simplified tax preparation

Payment gateways compatible with QuickBooks

The right payment gateway can easily boost your bottom line and improve the customer experience. With QuickBooks, there are several options to choose from. 

Gateways integrated with QuickBooks can help you handle payments from credit and debit cards, digital wallets, as well as bank transfers. The software even allows you to integrate multiple payment gateways to tailor to your customer needs. 

Of course, QuickBooks has its own gateway via QuickBooks Payments, which supports credit card and electronic transfers, and offers features like automatic payment reconciliation and recurring billing​.

But other popular options include:

  • Authorize.net
  • Braintree
  • CardConnect
  • GlobalPayments.
  • NMI
  • PayPal
  • Square​
  • Stripe
  • Veem

Streamlining Invoicing and Payment Collection

As mentioned above, integrating payment gateways with QuickBooks can automate your invoice creation. This helps to streamline your financial operations.

While the software has built-in features to automate invoice creations and several other accounting processes, integrated payment gateways can also automatically create and send an invoice in QuickBooks​ once a transaction is complete. 

Essentially, your customers can pay invoices directly through the gateway within your QuickBooks platform. 

At the same time, this greatly simplifies the payment collection process for your customers. With integrated payment gateways, you can offer seamless transactions, as customers pay directly upon purchasing, through a variety of payment options. 


Enhancing Customer Experience

It’s not just your business that can benefit from integrated payment gateways. They offer a number of benefits to your customers, too. 

Linking a payment gateway to your site makes it convenient for customers to order and pay in one place, without having to be redirected to a separate payment portal, especially if your gateway allows them to choose different payment options.  

Also, the added security of these integrations means that your customers can rest assured that their sensitive information isn’t being shared with or routed through an additional vendor. At the same time, because their information is stored directly on your site, customers can easily access detailed invoices and information about their purchase history. 

Finally, because the process is automated, your customers will not need to worry about mistakes on their invoices, or other inaccuracies such as buying something that is actually out of stock. This kind of assurance can go a long way in ensuring that you maintain a good reputation in the industry. 


Real-Time Financial Data Synchronization

Integrating payment gateways with QuickBooks helps to synchronize your payment data for real-time financial updates. This includes all the relevant transaction details, like payment amounts, dates, and customer information.

It starts with automated data entry. When customers pay through an integrated gateway, the transaction details are automatically recorded in QuickBooks. And as soon as the payment is processed, QuickBooks updates the associated invoice status to “Paid”, so your financial records are always current​.

Integration also allows you to immediately reconcile transactions, because as soon as a payment is made, it gets matched with a corresponding invoice.

Benefits of real-time financial updates

Having a current view of your overall finances has a number of benefits. For example, with minimal discrepancies between reported sales and actual payments received, you’ll have more accurate financial statements

It can also help improve your cash flow, in order to make better financial decisions and forecasts. Moreover, these integrations cut down on the amount of time your finance team spends on admin, because payment data is synced automatically. Overall, they allow for more streamlined operations. 


Managing Recurring Payments and Subscriptions

An added benefit of integrating a payment gateway with QuickBooks is the ability to set up and manage recurring billing for your subscription customers. All you have to do is set up a new recurring transaction template in QuickBooks, then ensure the option for ‘online payments’ is active once your payment gateway has been integrated. 

Your subscribers can then enter payment details which are stored for future transactions, and they’ll automatically be charged on the dates you specify in your template. 

Tracking and managing customer subscription details 

The most important part of managing your subscriber details is to regularly review all recurring transactions. This will help you ensure that the billing details are correct, and the schedules are up to date. Should you have any subscription changes or cancellations, you can adjust these on your template, to reflect with immediate effect. 

But what happens if the details are correct and your subscriber fails to pay, due to insufficient funds or a technological issue? One way to avoid this is to set up automated notifications in QuickBooks and your payment gateway to alert you of any discrepancies.

Then, you’ll need a process in place for how to manage these – whether that includes retrying the payment immediately, or sending a note to customers to update their information, if necessary.


Security and Compliance

Integrated payment gateways are a great way to process payments securely. In fact, gateways come with a number of security features, and must comply with the Payment Card Industry Data Security Standard (PCI DSS). Complying with PCI DSS standards guarantees a secure transaction environment and lowers the risk of fraud. 

However, depending on the gateway you integrate, it may come with one of many other kinds of additional security measures. These include:

  • Secure Sockets Layer (SSL), which establishes a secure connection between a payment provider and your customer’s web browser, to encrypt any transmitted data. 
  • Secure Electronic Transaction (SET). This is an encryption-based system developed by VISA and Mastercard. It ensures that all personal information associated with a card used to pay online is secure. 
  • 3D Secure. This provides an extra layer of authentication when customers make purchases, by prompting them to verify the transaction.  

It’s also possible to provide extra safety measures from your side. 

Best practices for maintaining data security and privacy

If your company uses integrated payment gateways, training your team is vital. They’ll need to know all about best practices for safeguarding customer data, including prevalent scams, and how to avoid them. 

You can also reach out to cybersecurity pros to help you conduct ethical hacking (or penetration testing). Here, they attempt to find any weak points in your site to help you ensure security.

As a worst-case scenario, you’ll need to establish protocols for what to do in the event of a security breach, to safeguard your data and prevent revenue loss. 


Selecting the Right Payment Gateway

Given the variety of payment gateways that are available for QuickBooks integration, it can be difficult to decide which one is best for your business. 

There are several factors to consider. For example, what each provider charges for transaction fees. These can either be set dollar amounts, or a percentage of total transactions. 

Then you’ll need to check out their security features, to ensure that your data is secure. Another thing to remember is customer support. In the event that you run into issues, you need them to be handled quickly and professionally. 


When in doubt, reach out to a professional to make sure you’re choosing the best option for your company. 


Implementation and Best Practices

Implementing a payment gateway is relatively straightforward. Simply navigate to the ‘apps’ section in QuickBooks and select your choice, then follow the prompts to link the two systems. 

However, keep in mind that you need to ensure that you include the correct API implementation to avoid compatibility issues. 

The best way to ensure a smooth integration between QuickBooks and your chosen payment gateway is to call in a professional. A dedicated team can ensure that you choose the right gateway. They will also be able to ensure that it’s fully integrated with your system, including any customizations you may need. With help from accounting software integration pros like Fusion CPA, you’ll also have access to troubleshooting and training for your team. 

If you need help integrating a payment gateway to QuickBooks, schedule a Discovery Call with one of our CPAs. With decades of experience, we can handle tricky integrations with ease. 


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The information presented in this blog article is provided for informational purposes only. The information does not constitute legal, accounting, tax advice, or other professional services. We make no representations or warranties of any kind, express or implied, about the completeness, accuracy, reliability, suitability, or availability of the information contained herein. Use the information at your own risk. We disclaim all liability for any actions taken or not taken based on the contents of this blog. The use or interpretation of this information is solely at your discretion. For full guidance, consult with qualified professionals in the relevant fields.