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6 BEST Credit Card Processing for QuickBooks in 2023

Dawn Prevete Dawn PreveteFinance Specialist October 18, 2023
October 18, 2023
The value a credit card processor brings to your business isn’t just based on affordable rates and a suitable pricing model. A good payment processor will also save you time on administrative tasks like accounting and invoicing, and a QuickBooks integration is an ideal way to do this.

Still, not every payment processor that offers this feature is a good choice. Some payment processors don’t have pre-built integrations, so you’ll need to know how to use APIs to build that connection yourself. Others charge extra for a QuickBooks integration on top of a sub-optimal pricing structure and high transaction fees.

You also don’t want to sign up with the cheapest credit card processing for QuickBooks only to find that you’re stuck with a faulty integration or hidden processing fees, and need to pay a few hundred dollars to escape your contract.

After researching dozens of options, I’ve found the best payment processing for QuickBooks available today. My top recommendation is Leaders Merchant Services (LMS). You’ll get a free QuickBooks integration included in your monthly fee, or you can pay for a unique two-way sync to share data in real time. 

Keep reading to find the best option for you and your business.

Short on Time? These Are the Best Credit Card Processing for QuickBooks in 2023

  1. Leaders Merchant Services – Comprehensive QuickBooks integration covers card, cash, e-check, and ACH transactions.
  2. PAYARC – Budget-friendly QuickBooks integration with two-way sync capability.
  3. ProMerchant – Easy integration with QuickBooks and zero-cost processing program for retail and restaurants.

See 3 More Great Options | Comparison Table

What We Look For in the Best Credit Card Processing Companies for QuickBooks

When I was researching payment processors, I made sure to keep the following features in mind:
  • Pre-built QuickBooks integration. Some credit card processors only allow you to set up integrations if you use their APIs to build them. Every processor on this list has a pre-built QuickBooks integration you can use, which will save you a lot of time (and headaches) when connecting your payment tools.
  • Competitive pricing. While different pricing structures work better for different types of businesses, I’ve made sure every processor on this list offers a reasonable fee structure. This includes any extra charges to integrate QuickBooks.
  • Great customer support. Setting up integrations isn’t always easy, particularly if you’ve never used payment software before. Every processor on this list offers friendly, helpful, and easy-to-access customer support to guide you through the process.
  • Developer toolkits. While all the processors on my list offer pre-built QuickBooks integration, having access to a developer toolkit gives you (or your developer team) the option to build custom payment software and integrations using pre-built APIs and SDKs. The best toolkits also have plenty of documentation on how to connect your software to your processor’s software.
  • Compatibility. Every payment processor on this list uses QuickBooks integrations that are regularly updated to ensure they work with the latest version of the software. In addition, I’ve made sure that each QuickBooks integration supports multiple legacy versions of QuickBooks.

A Quick Note on QuickBooks Integrations

There are multiple versions of QuickBooks available, with the most common being QuickBooks Online, QuickBooks Desktop, and QuickBooks Desktop for Mac. Each of these products have multiple versions. Not all QuickBooks integrations work with every version. While I refer to all these products as “QuickBooks” for ease within this article, I’ve noted where integrations don’t support specific QuickBooks software versions.

Leaders Merchant Services (LMS) is one of the most affordable payment processors for small and low-volume merchants. LMS helps you to grow your business with affordable interchange-plus rates and custom pricing, so it’s an ideal choice for businesses in their growth phase. On top of this, you’ll also get Instant Accept for QuickBooks.

Instant Accept automatically logs accepted transactions in QuickBooks, so you won’t have to worry about manually inputting data. And unlike most other QuickBooks integrations, Instant Accept covers cash, card, e-check, and ACH transactions. Through your POS software, you’ll also be able to search any data stored in QuickBooks.

The only downside is that Instant Accept is not included with LMS’s monthly fee, so you’ll have to pay an extra monthly fee, a one-off setup fee, and a small fee per transaction. Still, if you regularly use QuickBooks and process a large volume of transactions, the time you’ll save on administrative tasks will more than make up for the added cost.

Features and Benefits

  • Interchange-plus pricing. LMS offers some of the lowest interchange-plus rates around. On top of that, you’ll pay a monthly fee depending on what other features you need. This means you’re only paying for what you need.
  • Merchant cash advances. If you need some financial support to grow your business, LMS offers cash advances that you’ll repay through a small commission on future sales.
  • High approval rate. LMS approves 98% of merchants. What’s more, it aims to have your account set up and ready to accept payments on the same day you apply.
  • Modern e-commerce software. LMS also offers the industry-leading Authorize.net payment gateway, which comes with advanced fraud detection and prevention tools, additional software integrations, and more.
Read our Leaders Merchant Services review to see how it can help grow your business.

QuickBooks integration fee From $39.96/month, plus setup fees and a small fee per transaction
Additional integrations 140+ via Authorize.net
Customer support 24/7 phone support
Transaction fees on cheapest plan ~2% + 0¢
Monthly fee on cheapest plan $9.00

Given PAYARC’s commitment to tailoring plans and features to a business’s unique needs, it’s no surprise that it offers plenty of choice when it comes to integrations. Through its partnership with Chargezoom, you can integrate QuickBooks Online or Desktop and enjoy two-way sync for one of the lowest rates on the market.

Chargezoom lets you batch load credit cards with a click and set up automated or recurring billing. Every payment type — debit cards, credit cards, ACH, and eCheck — is reconciled in QuickBooks instantly, eliminating the time-consuming tasks of manual entry or CSV file upload and freeing you and your staff to focus on growing your business.

With Chargezoom, Payarc offers one of the cheapest QuickBooks integrations starting at just $9 per month. In addition to two-way syncing, you’ll get other great features like unlimited branded e-invoicing, email payment links, and a credit card vault.

Features and Benefits

  • Integrated reporting and analytics. You can analyze transaction data, track sales, and monitor payment performance directly from your QuickBooks or PAYARC dashboard.
  • Fraud prevention and risk management. PAYARC incorporates advanced fraud prevention tools and risk management measures to protect merchants from fraudulent transactions. PCI compliance, tokenization, and end-to-end encryption ensure your funds and customer data is secure.
  • Modern payment software. PAYARC offers impressive technology-driven features for managing your business, including built-in invoicing, data-driven reports, and real-time sales and payment tracking.
  • International commerce. Through its partnerships with global payment gateways, Payarc allows you to market products and services to an international clientele. By expanding your market reach, you can maximize sales and profits.
Read our full Payarc review for more details.

QuickBooks integration fee $9 – $59 per month
Additional integrations 12+
Customer support 24/7 phone, email, and social media
Transaction fees on cheapest plan 2.49% + 30¢ (in-person)
Monthly fee on cheapest plan N/A

ProMerchant offers two pricing models: interchange-plus and zero cost processing, although its zero cost plan is only available for restaurant and retail-based businesses. Plans are month-to-month, so you’ll never have to worry about hefty cancellation fees. Approval is also fast and easy – you can expect a response in as little as two hours.

You can set up a QuickBooks integration through the Authorize.net payment gateway, so you can automatically sync your daily transactions with QuickBooks for easy credit card reconciliation. You can also automate recurring billing and send emails to customers with a convenient “click to pay” link.

It’s worth noting that ProMerchant promises to never raise the transaction fee on its interchange-plus plan even if its costs increase, which can make it much easier to project your long-term processing costs.

Features and Benefits

  • Next-day funding. Funding for every transaction processed by 8:30 PM is released to your bank account the next day. Unlike other processors, ProMerchant offers this as a standard feature – there’s no additional charge.
  • Customer relationship management (CRM) tools. Integration with popular CRM software gives you tools to organize customer data, track interactions, and automate communications. This can help you build rapport with your clientele and boost retention rates.
  • Excellent customer support. From the day you’re approved, ProMerchant will assign you an Account Manager and dedicated support team to address any issues or questions. Support is available 24/7 by phone or email.
  • Inventory management. ProMerchant’s built-in tools make managing inventory for your store or restaurant easy. You can organize, track, and update product listings, plus monitor stock levels and enable automatic notifications for low inventory.
To learn more, read our full ProMerchant review.

QuickBooks integration fee Varies (monthly fees from Authorize.net)
Additional integrations 100+ integrations via Authorize.net
Customer support 24/7 phone support
Transaction fees on cheapest plan 3% + 10¢ (credit)
Monthly fee on cheapest plan $7.95

4. Flagship Merchant Services: Connect QuickBooks to Your E-Commerce Store

The beauty of Flagship Merchant Services is that it doesn’t offer a one-size-fits-all solution. Instead, you’re encouraged to negotiate the best deal for your business. Because these interchange-plus and tiered pricing models aren’t set in stone, you’ll only have to pay for the features you need – you won’t have to pay for a fixed plan based on your industry or business size.

While you’ll be able to connect QuickBooks to your e-commerce store without having to build a custom integration, there are no direct integrations that connect Flagship to QuickBooks. Instead, you’ll have to use Commerce Sync to connect QuickBooks to the Authorize.net payment gateway, and then connect Authorize.net to Flagship (which will be set up for you).

While the cost of Commerce Sync isn’t as high as other QuickBooks integrations on the market, it’s only worth it if your business primarily takes payments online or over the phone.

Features and Benefits

  • Same-day funding. If you need quick access to your funding, Flagship offers a same-day funding option for an additional cost. Otherwise, you can expect to receive your money within a few business days.
  • Quick setup. Once your application has been approved, Flagship can have your merchant account up and running in only a few hours, which is ideal for new businesses.
  • iAccess Business Management software. This reporting and analytics software, included in the monthly fee, empowers you to evaluate your business’s performance compared to local businesses and those of similar size in your industry. Moreover, it enables you to create sales summaries, allowing you to closely track your business’s financial well-being.
  • Free hardware. Depending on the contract you sign, you’ll be able to get a free terminal. Certain contracts are even eligible for free Clover devices. These devices aren’t cheap, so getting one for free is a huge advantage if you need state-of-the-art payment hardware.
Our in-depth Flagship Merchant Services review has more great features.

QuickBooks integration fee From $14.95/month
Additional integrations 140+ via Authorize.net
Customer support 24/7 phone support
Transaction fees on cheapest plan 1.58% + 19¢ (in person)
Monthly fee on cheapest plan $7.95

Stax’s all-in-one payments platform is designed for high-volume businesses that need modern payment software, so it’s no surprise it offers two options for easy QuickBooks integration. The first is available on the Pro plan and above, and it simply syncs your sales data with QuickBooks to save time on your accounting tasks.

On top of that, Stax offers a two-way data sync with QuickBooks Online so no matter where your payment data originates, it’ll be shared in real time between your payment software tools. It also syncs your customer, inventory, and invoicing data. While this option costs an extra $39/month (and only works with QuickBooks online), it really is invaluable if you use QuickBooks’ invoicing feature to accept payments.

Although the advanced integration is one of the most expensive options on this list, Stax offers some of the lowest processing fees of any processor. Instead of taking a cut of every transaction, it charges a flat monthly subscription fee. As a result, you could save up to 40% on payment processing with Stax, with more savings the more you process.

Features and Benefits

  • Modern payment software. Your Stax monthly fee includes multiple software tools. The lowest tier plan includes CRM software, analytics and reporting, and invoicing. As you move up to higher tiers, you’ll also gain access to features like payment links, a card vault, one-click shopping carts, and more.
  • Transparent subscription-style pricing. Stax charges a flat monthly fee, zero interchange markup, and a small flat transaction fee, making it easy to budget for your monthly bill.
  • Plenty of valuable integrations. On top of the QuickBooks integration, you’ll be able to connect your Stax software to other tools like BigCommerce, Mailchimp, Asana, and more.
  • Developer toolkit. If you need to add more capabilities to the built-in QuickBooks integration or even build a custom solution, Stax’s developer toolkit provides everything you need. You’ll get a library of APIs and SDKs to use, as well as detailed documentation to help you along the way.
Read more about Stax’s software in our expert review.

QuickBooks integration fee Free (one-way), $39/month (two-way sync)
Additional integrations 15+
Customer support Live chat, email, web forms/tickets, phone, and fax
Transaction fees on cheapest plan 0% + 10¢ (in-person)
Monthly fee on cheapest plan $99.00

6. PaymentCloud: Affordable QuickBooks Integration for High-Risk Businesses

PaymentCloud is a top choice for mid- to high-risk merchants – but that doesn’t mean it’s not a good option for any type of business, whatever its risk level. It offers affordable interchange plus, fixed rate, and zero-cost credit card processing plans that suit a range of industries and business needs.

What’s more, you can connect QuickBooks (Online or Desktop) to streamline your financial management. Transactions are automatically synced between PaymentCloud and QuickBooks. You can easily create invoices, issue checks, reconcile bank accounts, track accounts receivable, and generate a wide variety of custom financial reports in one place.

PaymentCloud offers several ways to integrate QuickBooks, though Chargezoom is its top recommendation. Your monthly cost will depend on the Chargezoom plan you choose.

Features and Benefits

  • Multiple funding options. From working capital loans to business lines of credit and industry-specific loans, PaymentCloud offers flexible financing opportunities if you need a cash injection.
  • Practical integrations for your business. In addition to QuickBooks, you can integrate 170+ other useful products, from popular e-commerce platforms like Shopify and WooCommerce to marketing, inventory, and customer management tools.
  • Multiple payment gateways. PaymentCloud provides an option of 14 all-compatible, PCI-secure payment portals, such as Authorize.net Cybersource, Stripe, and PayPal.
  • Advanced security. When it comes to fraud and chargeback protection, PaymentCloud offers its merchants free tools to help you mitigate fraudulent transactions. Specific recommendations may include tokenization, address verification (AVS), card verification value (CVV), IP tracking, and more.
Learn more about PaymentCloud in our in-depth review

QuickBooks integration fee $9 – $59 per month
Additional integrations 170+
Customer support 24/7 phone support
Transaction fees on cheapest plan Around 2.1% + 15¢
Monthly fee on cheapest plan $14.00

These Are the Best Credit Card Processing for QuickBooks

Connecting your payment software to QuickBooks usually comes at an additional cost each month. If your business has a limited budget, you need to be sure that the money you spend ultimately saves you time and effort – and if it can automate your bookkeeping process, all the better.

Overall, Leaders Merchant Services provides the best balance of cost and utility. It offers Instant Accept by QuickBooks, which automatically syncs all sales data – including cash, card, ACH, and e-check transactions

If you’re concerned about how much you’re spending on payment processing, then take a look at PAYARC. You’ll get affordable subscription-style pricing, no interchange markup, and fantastic QuickBooks integration with two-way sync for a low monthly fee.

If you’re in the retail or restaurant industry, I’d recommend ProMerchant. This payment processor offers an affordable QuickBooks integration and features two pricing models, including a zero-cost processing plan.

Here’s a quick summary of the best QuickBooks payment integrations:

Best Feature Best For Monthly fee on cheapest plan Transaction fees on cheapest plan
Leaders Merchant Services Instant Accept by QuickBooks automatically logs any payment data entered into your POS software Businesses that take most of their payments in-person $9.00 ~2% + 0¢
PAYARC Budget-priced QuickBooks integration with two-way sync Businesses that want a tailored approach to a QuickBooks integration N/A 2.49% + 30¢ (in-person)
ProMerchant Secure QuickBooks integration with industry-leading Authorize.net payment gateway Restaurants and retail businesses that want budget-friendly payment processing $7.95 3% + 10¢ (credit)
Flagship Merchant Services Great QuickBooks integration for e-commerce businesses Businesses that primarily make sales online or over the phone $7.95 1.58% + 19¢ (in person)
Stax QuickBooks two-way sync to quickly integrate all your payment data High-volume businesses that take payments through QuickBooks $99.00 0% + 10¢ (in-person)
PaymentCloud Multiple options and pricing options for QuickBooks integration Mid- to high-risk businesses looking for affordable processing $14.00 Around 2.1% + 15¢


Can you use other merchant services with QuickBooks?

Yes! QuickBooks doesn’t lock you into using its own payment processing service, so you can use another processor that works for your business. Before you choose a payment processor, make sure you know what features to look out for. Leaders Merchant Services offers low interchange-plus pricing and customer plans so you only pay for the features you need.

Does Square POS link to QuickBooks?

Yes, Square POS has a pre-built integration for QuickBooks. However, QuickBooks Desktop doesn’t support Square’s Split Tender or Multiple Locations feature, which isn’t ideal for larger businesses or restaurants. That’s why we don’t recommend Square for QuickBooks. If you’re a larger business looking to fully automate your accounting process, I recommend PAYARAC’S two-way data sync integration.

How do I avoid credit card fees in QuickBooks?

To avoid QuickBooks’ high payment processing fees, you’ll want to use payment processor that’s better suited for your business and can provide you with additional tools. If you want to avoid credit card fees (almost) entirely, then take a look at National Processing. On top of its QuickBooks integration, ProMerchant offers a  zero cost processing plan where you pay a low monthly fee and no per-transaction fees.

Can I use QuickBooks to process credit cards?

You can, but I don’t recommend it. QuickBooks charges a high per-transaction rate, and the rate you pay will depend on whether you’re using QuickBooks Online or QuickBooks Desktop. Compared to our top 10 credit card processors in 2023, QuickBooks’ payment processing service doesn’t offer great value for your money.

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