Best Merchant Accounts for Quickbooks Integration

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How To Integrate Third-Party Merchant Accounts With Quickbooks

Intuit's QuickBooks accounting software is by far the most popular do-it-yourself bookkeeping program available for small business owners. Launched in 1994, the service has since become a household name with a market share above 80% and an entire suite of specialized business solutions. If you use QuickBooks and also accept credit cards through QuickBooks Payments, you might have discovered that your processing fees are very high. QuickBooks seems to believe that it should charge businesses a premium for the ease of use of having accounting and payments under the same roof. In fact, the QuickBooks Payments statements we have seen contained some of the highest fees in the industry (See: Merchant Account Fee Auditing).

Quickbooks Credit Card Processing Integration is Possible

QuickBooks resisted allowing third-party payment integration for a long time. After enough pushback by customers and the threat of more open competing account software providers, QuickBooks finally opened up its platform to outside credit card processing. Not all merchant accounts support direct QuickBooks integration, and among those that do, there aren't many competitively priced options.

In a Rush?
Our top choice for Quickbooks payment integration is Helcim because it has the easiest method while also being the lowest cost credit card processor in this list. Learn more about Helcim's Quickbooks integration.

Quick Pick List of Payment Processors That Can Integrate With Quickbooks:

  1. Helcim
  2. CDG Commerce
  3. Shopify
  4. Host Merchant Services
  5. PaymentCloud

How to Select the Best Quickbooks Credit Card Processor

When selecting the best credit card processor for a Quickbooks Integration in the USA, there are several factors to consider, which we have included below.

Seamless Integration with Quickbooks

The credit card processor should integrate seamlessly with Quickbooks using their own technology or through proven third-party gateways, allowing for easy and efficient payment processing and bookkeeping. Often, processors will promote that they integrate with Quickbooks but the reality is that they only offer several manual steps to importing the data each time it needs to be added to the accounting software.

Credit Card Processing Fees and Rates

Credit card processors charge a range of fees and rates, including transaction fees, monthly fees, and processing fees. Business owners should look for a processor with competitive rates and fees that align with their budget and transaction volume. All of the picks below offer the best pricing in the industry.


Security is a crucial consideration for any business handling sensitive financial information. The credit card processor should offer robust security features, such as encryption and fraud protection, to ensure the safety of customer and business data.

Reliable Customer Support

Owners should look for a credit card processor that offers reliable and responsive customer support. This is particularly important for businesses that rely heavily on payment processing and need immediate assistance with any issues that arise. All of the picks below have a reputation for providing excellent support.

Reputation and Reviews

It's important to research the reputation and reviews of potential credit card processors. Look for providers with positive customer feedback, high ratings, and a track record of delivering quality service to their clients. Each of the processors below have top ratings across the board.

Methods For Syncing Third-Party Transactions with Quickbooks Online

There are various ways to get your credit card transaction into Quickbooks Online. Unfortunately, none of them are as seamless and Intuit's own payment integration, but the savings achieved with a third-party processor can outweigh the cost of additional accounting steps for importing the sales.

Direct Integration Through QuickBooks-Compatible Apps and Plug-ins

Numerous third-party credit card processing services offer dedicated apps or plugins specifically designed for compatibility with QuickBooks Online. These apps simplify integration by connecting your credit card processing service directly to QuickBooks Online, allowing for seamless data transfer and transaction synchronization. To integrate these services, your processor will need to have its own app or plugin for communicating with Quickbooks Online. This is usually the best way to integrate payments with Quickbooks because everything is handled by your processor, which means no other third-party fees.

Third-Party Quickbooks Direct Integration Gateways

Gateway providers function as intermediaries between your credit card processing service and QuickBooks Online. They facilitate data exchange between the two systems, ensuring that your transactions are recorded accurately in your accounting software. Some common gateway providers compatible with QuickBooks Online include, Melio, and Third-party gateways come with their own fees and nuances that will need to be considered. The benefit of working with a gateway provider is that you can switch your credit card processor without also needing to change your method of Quickbooks payment syncing integration.

Manual Import of Transaction Data

In some instances, businesses may opt to manually import transaction data from their credit card processing service into QuickBooks Online. To accomplish this, you'll need to export transaction data from your processing service (usually in the form of a CSV or Excel file) and then import the file into QuickBooks Online. While this method requires more manual effort, it offers a solution for businesses that use credit card processing services without direct integration options or gateway providers.

Custom Software Integration with Quickbooks API

QuickBooks Online API documentation provides guidelines for developers to send sales information from a third-party credit card processing service to QuickBooks Online. The process typically involves the following steps:

  1. Authentication: Before sending any data, you need to authenticate your application with QuickBooks Online using OAuth 2.0, which enables secure access to the QuickBooks Online API. This process will require you to obtain an access token and a refresh token.
  2. Creating an Invoice or Sales Receipt: To send sales information from a third-party credit card processing service, you'll need to create an Invoice or Sales Receipt in QuickBooks Online. The API documentation provides detailed information on how to create these entities using JSON payloads, specifying required fields such as customer information, item details, and transaction amounts.
  3. Associating Payments with Invoices or Sales Receipts: Once you've created an Invoice or Sales Receipt, you'll need to associate the payment information from your third-party credit card processing service with the transaction. This involves creating a Payment object through the API, specifying the related Invoice or Sales Receipt and the payment method, amount, and other relevant information.
  4. Error Handling and Validation: The API documentation also covers error handling and validation, ensuring that your application can handle any issues that may arise during data transmission. This includes managing API response codes, checking for errors, and validating data before sending it to QuickBooks Online.

By following the guidelines provided in QuickBooks Online API documentation, developers can effectively send sales information from third-party credit card processing services to QuickBooks Online, ensuring seamless integration and accurate financial reporting.

Who to Choose for QuickBooks Credit Card Processing Integration

We've researched and selected top rated credit card processors and that also offer QuickBooks integration. The following merchant services providers offer either direct integration or indirect integration. Providers with direct integration offer solutions like payment gateways, plugins, or APIs that seamlessly transfer your transaction details and payment history from your merchant account to QuickBooks. Providers with indirect integration can still be used with QuickBooks, but they may require you to take extra steps such as manually uploading reports or signing up with a third-party service. Each description below will provide further insight.

#1 Merchant Account for QuickBooks

helcim logo


Lowest Cost, Most Direct, and Easiest Method

Helcim has its own plugin for integrating with Quickbooks Online. Its custom plugin not only makes it one of the easiest and most seamless methods, but Helcim is also one of the lowest cost and most versatile credit card processors in the industry. The company serves most business needs and offers a unique volume-based rate and fee model wherein the processing fees reduce as a business' sales grow. The company also charges no monthly or annual fees, and does not lock businesses into long-term contracts. Integrating Helcim into Quickbooks is a simple process summarized below:

  • Connect Helcim to QuickBooks Online: To begin the integration, users must connect their Helcim account to QuickBooks Online. This process typically involves signing in to the Helcim dashboard, navigating to the “Integrations” section, and selecting QuickBooks Online. Users will then be prompted to sign in to their QuickBooks Online account to authorize the connection.
  • Configure Sync Settings: Once connected, users can configure their sync settings in Helcim. This includes choosing the frequency of data synchronization (e.g., daily, weekly, monthly), selecting the appropriate accounts and tax rates to be used in QuickBooks Online, and mapping payment methods from Helcim to QuickBooks Online.
  • Synchronize Transactions: With the sync settings configured, Helcim automatically synchronizes transaction data, including sales, refunds, and fees, with QuickBooks Online. This process ensures that the transaction data in QuickBooks Online remains up-to-date and accurate without manual intervention.
  • Review and Reconcile: After the synchronization is complete, users can review and reconcile their transactions in QuickBooks Online. This involves verifying the accuracy of the imported data and ensuring it aligns with their financial records.

Helcim simplifies the process of integrating with QuickBooks Online by providing an easy-to-use connection and synchronization system. Users can efficiently manage their transaction data by configuring sync settings, automating the synchronization process, and reviewing their financial information within QuickBooks Online. Helcim is also the most cost-effective provider we found for Quickbooks integration during our research.

Get the details on Helcim's integration with Quickbooks here.

cdg commerce logo

CDG Commerce

Best for Gateway and Plugin Selection

CDG Commerce takes a top position for QuickBooks payment integration as one of the best choices for integrating credit card payments and accounting. This provider can assist businesses with various integration options such as determining the appropriate payment gateway for third-party paid and free software plug-ins as well and assist in custom software integrations via APIs and developer tools. CDG Commerce, however, does not have a direct integration with QuickBooks Online.

Here's a general outline of how the integration process might work using CDG Commerce and third-party gateway provider:

  • Compatible gateway provider assistance: Your CDG Commerce representative will help you select a third-party gateway based upon you businesses point-of-sale needs.
  • Connect CDG Commerce to the gateway provider: Once you have selected a suitable gateway provider, you will connect your CDG Commerce account to the provider. This usually involves signing in to your gateway provider's platform, adding CDG Commerce as a payment processor, and entering the necessary API credentials and account information.
  • Connect the gateway provider to QuickBooks Online: After connecting CDG Commerce to the gateway provider, you will establish a connection between the gateway provider and QuickBooks Online. This typically involves signing in to your QuickBooks Online account through the gateway provider's platform and authorizing access.
  • Configure sync settings: With both connections established, you can configure the sync settings within the gateway provider's platform. This may include selecting the frequency of data synchronization, mapping payment methods and accounts, and setting up tax rates.
  • Synchronize transactions: Once the sync settings are configured, the gateway provider will automatically synchronize transaction data, including sales, refunds, and fees, from CDG Commerce to QuickBooks Online. This ensures that your financial records in QuickBooks Online remain up-to-date and accurate.
  • Review and reconcile: After the synchronization is complete, you can review and reconcile your transactions in QuickBooks Online, verifying the accuracy of the imported data and ensuring it aligns with your financial records.

Approves Most Business Types

Not only does CDG Commerce make is easy to integrate with QuickBooks, but the company serves most industries and provides a broad array of services to meet the needs of both e-commerce and brick-and-mortar businesses. The company has very highly rated 24/7 costumer support and has maintained a near perfect score since we first reviewed CDG Commerce nearly 10 years ago. Business owners looking to move away from QuickBooks Payments are well-advised to consider CDG Commerce.

Get the details on Integrating CDG with Quickbooks here.

Additional Quickbooks Integration Options

shopify logo


E-Commerce Made Easy

Shopify is a great solution for e-commerce merchants who may or may not maintain physical storefronts. In addition to an endlessly customizable online store experience, Shopify offers chargeback recovery, email marketing, rewards programs, and an iPad-based point-of-sale application that merchants can use to accept payments in-person. Shopify offers month-to-month pricing plans with variable pricing and product tiers.

Shopify + QuickBooks

Integrating with QuickBooks through Shopify can only be accomplished via a third-party plugin. As a result, your experience with using QuickBooks through Shopify will vary depending on which plugin you select. Fortunately, the Shopify App Store has an entire section devoted specifically to different QuickBooks integration solutions, complete with reviews and descriptions of each plugin. Merchants can select which one is most appealing in terms of features, pricing, and user feedback, and some even include free trial periods.

Shopify Reviews

Shopify is headquartered in Ottawa, Ontario, and has been in operation since 2005. The company provides phone, email, and live chat support to all of its merchant tiers and enjoys very few online complaints despite its massive user base. The BBB gives Shopify an “A+” rating at this time, while awards the company an “A.”

For more information, see the Shopify website.

Host Merchant Services logo

Host Merchant Services

Long-standing Top Rated Merchant Account

Host Merchant Services deserves a spot on this list because it has consistently ranked as one of the most transparent, affordable merchant account providers on ever since our first review of the company. Additionally, the company has received a dozen or so positive testimonials online and only a handful of public complaints in its entire history.

Host Merchant Services + QuickBooks

Host Merchant Services offers QuickBooks integration through its Verosa Gateway. Verosa’s payment terminal for Quickbooks integrates with QuickBooks Pro, Quickbooks Premier, Quickbooks Enterprise, or Quickbooks Accountant. Adding a USB card swiper allows you to take “in-person” payments and avoid higher “card not present” rates. Host Merchant Services does not specifically charge extra for QuickBooks integration, but merchants should be sure to inquire about any potential costs that are associated with adding a payment gateway or integrating other necessary features.

Host Merchant Services Reviews

Founded in 2009, Host Merchant Services is headquartered in Newark, Delaware. The company offers phone and email support. Host Merchant Services currently has an “A+” rating with the Better Business Bureau (BBB) and an “A+” rating with

For more information, see the Host Merchant Services website or call (888) 727-4538

PaymentCloud Logo


High Risk Specialists

PaymentCloud is one of the most highly rated providers on CPO. They score highly in our review due to its exceptionally low amount of customer complaints in the short time the company has been in operation. PaymentCloud has been well known in the industry to cater to high risk merchants since its inception. Even if you're not in a high risk industry, PaymentCloud rates well as an overall payment provider.

PaymentCloud + Quickbooks

This provider can integrate in to Quickbooks' accounting software seamlessly and provides industry-specific solutions that help tailor the software to the merchant's needs. PaymentCloud says this helps provide lower rates as well as better automation and integration for the Quickbooks platform.

PaymentCloud Reviews

Founded in 2015, PaymentCloud is based in Woodland Hills, California. The Better Business Bureau (BBB) does not provide a rating for PaymentCloud, but gives the company an “A+.”

For more information, see the PaymentCloud website or call (888) 506-7859.

Final Thoughts

When selecting a third-party credit card processor to integrate with QuickBooks Online accounting software, business owners must carefully consider a variety of factors to ensure a seamless and efficient integration that caters to their unique requirements. Compatibility is of utmost importance, as it is crucial to choose a processor with a proven integration with QuickBooks Online, either through apps or plugins, or compatibility with third-party gateway providers.

Additionally, business owners should assess the transaction fees and pricing structure of the processor, taking into account not only the cost per transaction but also any monthly fees or additional charges that may apply. The ease of integration and setup is another significant factor, as a straightforward and user-friendly integration process can save valuable time and resources. Moreover, the level of customer support and assistance provided by the processor can greatly impact the overall user experience, making it essential to evaluate the quality and responsiveness of their support services.

Lastly, considering the processor's ability to handle various payment methods, currencies, and international transactions is crucial for businesses with diverse clientele or plans for global expansion. By taking these factors into account, business owners can make an informed decision when selecting a third-party credit card processor to integrate with their QuickBooks Online accounting software, ultimately enhancing their payment processes and overall financial management.

Frequently Asked Questions:
Quickbooks Credit Card Processing

What are merchant accounts for QuickBooks integration?

Merchant accounts for QuickBooks integration are financial services that seamlessly connect with Intuit's QuickBooks accounting software. These accounts enable businesses to accept credit card and electronic payments from their customers and automatically sync the transaction data with QuickBooks, streamlining payment reconciliation and financial reporting.

Why do businesses need specific merchant accounts for QuickBooks integration?

Specific merchant accounts designed for QuickBooks integration offer a more efficient and automated payment processing experience. They eliminate the need for manual data entry, reduce errors, and provide accurate real-time financial reporting within the QuickBooks ecosystem.

How can I find the best merchant account provider for QuickBooks integration?

To find the best merchant account provider for QuickBooks integration, consider the following steps:

a. **Research QuickBooks-Compatible Providers:** Look for payment processors that specialize in serving businesses using QuickBooks. These providers will have experience in integrating their services with QuickBooks and can offer seamless connectivity.

b. **Verify Integration Features:** Ensure that the merchant account provider offers full integration with your version of QuickBooks, allowing for automatic transaction synchronization and payment reconciliation.

c. **Check for Multi-Channel Support:** If your business accepts payments through multiple channels (e.g., in-person, online, mobile), choose a merchant account that can integrate with all relevant payment channels to streamline your financial data.

d. **Compare Transaction Fees and Rates:** Assess the processing fees, transaction rates, and any other costs associated with each potential merchant account provider. Choose a provider with transparent and competitive pricing that aligns with your business's size and transaction volume.

e. **Check for Security Measures:** Verify that the merchant account provider offers secure payment processing and adheres to Payment Card Industry Data Security Standard (PCI DSS) requirements to protect sensitive payment data.

Can businesses use regular merchant accounts for QuickBooks integration?

While businesses can use regular merchant accounts for payment processing, they may require additional manual efforts to reconcile transactions in QuickBooks. Specific merchant accounts with QuickBooks integration capabilities offer a more streamlined and automated solution.

Are there any specific considerations for different business types using QuickBooks integration?

Different businesses may have unique needs when it comes to QuickBooks integration. For example, retail businesses may require point-of-sale integration, while service-based companies may prioritize online payment integration. Consider your specific business type and requirements when choosing a merchant account provider.

How long does it take to set up a merchant account for QuickBooks integration?

The time it takes to set up a merchant account for QuickBooks integration can vary depending on the provider and your business's specific circumstances. The setup process may involve a few days to a couple of weeks to ensure a smooth integration with your QuickBooks software.

Can businesses accept international payments with a merchant account for QuickBooks integration?

Yes, many merchant account providers for QuickBooks integration offer support for international payments, including multi-currency transactions, which can be beneficial for businesses with a global customer base.

Can businesses process both one-time payments and recurring billing with a merchant account for QuickBooks integration?

Yes, merchant accounts for QuickBooks integration typically support both one-time transactions and recurring billing, allowing businesses to manage various payment scenarios within their accounting software.

 Are there any hidden fees I should be aware of when choosing a merchant account for QuickBooks integration?

Carefully review the contract terms and fees of potential merchant account providers to identify any hidden costs. Watch out for setup fees, monthly minimums, and any other charges that might impact your overall costs.

Can businesses switch merchant account providers for QuickBooks integration if they are not satisfied with the service?

Yes, businesses can switch merchant account providers for QuickBooks integration if they are not satisfied with the service or find a better fit for their specific needs. However, be mindful of any contractual obligations and potential termination fees that might apply.

Finding the best merchant account provider for QuickBooks integration is essential for automating your payment processing and financial reporting tasks. Take the time to research and compare different options to choose a provider that offers seamless integration with QuickBooks and meets your business's payment processing requirements.

Reader Comments

Tell Us What You Think

11 User Reviews

  • Frankie

    I’m reaching out to express my sincere gratitude for your thorough and insightful article on “Best Merchant Accounts for Non-Profits”. As a part of a non-profit organization, your guide has been incredibly helpful in assisting me to understand and navigate this specific sector.

    Your detailed analysis of each merchant account, emphasizing their unique benefits, potential challenges, and standout features, was professionally executed. You’ve managed to break down complex subjects into a format that’s easily understandable for readers like me.

    I particularly appreciated your focus on key factors such as transaction fees, customer service, and security measures. Your insights into the specific needs of non-profit organizations, including managing donations, integrating with fundraising software, and ensuring regulatory compliance, were incredibly useful.

    It’s clear that your guide is the product of deep research, time, and industry expertise. Your dedication to providing accurate, relevant, and practical information has greatly simplified the often complex decision-making process, enabling professionals like me to make more informed decisions.

    Thank you once again for your valuable contribution to this field. Your hard work, dedication, and expertise are greatly appreciated.

  • uptoWord

    I’m glad to see that there are still good merchant accounts available for Quickbooks integration. I’m looking for one that will be able to handle a lot of transactions and have a low fee.

  • QuickBooks Error 100


    The information is really helpful, but it needs to be updated with information on EMV compliance. As far as I can tell none of these solutions are capable and there’s no way for me (or anyone) in my organization without significant funds or resources at their disposal would ever get this done within a reasonable time frame.

  • Nick S.

    We use QBO to automate monthly sales receipts that charge to a credit card. Other than Intuit’s merchant services, can any other merchant / gateway integrate directly into QBO? The non-swipe transaction fees are high.

  • Peggy Meisch

    We are looking for a merchant account that is compatible with Quickbooks Point of Sale. Only one of those listed mentions QB POS, and that is to say that it does NOT work with it. As a non-profit organization, we need a cheaper solution than going through Intuit and paying their exorbitant charges. Suggestions? Thanks.

    • CPO

      Hi Peggy,

      There is no approved way to fully integrate a third-party merchant account directly with QuickBooks Point of Sale at this time (see this FAQ page). It is possible to link a third-party payment processor to QuickBooks Point of Sale, but you will have to manually enter transaction information into QuickBooks every time you process a payment. This may be okay for your organization if you do not have a highly active sales/donation environment. However, it will require extra work for each transaction and will not function like a fully integrated system (i.e. automatically tracking the payments for you in QuickBooks).

  • MIke

    Good info, but list should be updated with information on EMV compliance. As far as I can tell, none of these solutions are EMV capable. I found [Redacted – restricted promotional content] to have a EMV capable solution (we are using their non EMV compliant solution right now), but cost of switching is expensive. I was hoping to find a less expensive solution that integrates directly with QBPOS.

    • Phillip CPO

      Hi Mike, all of the providers in this list either offer EMV compliant hardware or have announced that they will accept liability for any fraudulent transactions run through their non-compliant hardware (at least until they have a compliant solution). Unfortunately, as of the posting of this reply, Intuit does not allow any third-party merchant account integrations with QBPOS. As a proprietary POS system, they have restricted merchants to using Intuit Merchant Services. If you wish to switch away from Intuit Merchant Services, you’ll either be forced to find a different POS or use a standalone terminal in conjunction with the POS and manually enter the sale in QBPOS.

      I hope this helps you with your question. Best of luck with your business!

      • Intuit customer

        The point Phillip makes is a moot one. Although Intuit may claim they’ll accept responsibility for fraudulent claims and you pay their (handsome) PCI fees, the reality is; when push comes to shove and you have an issue, Intuit tells you to work it out with the customer (they won’t intervene ). In any dispute escalated for further review they charge the merchant a $500 fee per transaction to arbitrate. Meanwhile they hold your funds in limbo for 90 days. So intuit really doesn’t have any incentive to resolve fraud or disputed issue either way (and the customer is always wrong at Intuit ). Intuit always ride the elevator… you take the shaft.

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