Intuit Merchant Services Review: Is This System Right for Your Business?

Intuit merchant services offer top-tier payment and transaction management operations to small businesses that already use Intuit products.

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Intuit merchant services fly a bit under the radar. Sure, every small-business owner knows of Intuit thanks to its nearly ubiquitous accounting software, QuickBooks. But what you might not know is that Intuit also offers a suite of merchant services to help small-business owners manage transactions. In fact, Intuit took its dexterity for small-business finances and applied it with equal skill to their QuickBooks merchant services products — which include QuickBooks Payments and QuickBooks Point of Sale.

From affordable processing fees to accessible merchant center, Intuit merchant services offer top-tier payment and transaction management operations to small businesses like yours. And because they know that the most important thing a business owner can have is options, Intuit merchant services come in multiple versions for you to choose from.

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Intuit merchant services caveats

Before we cover the details on all the various iterations of Intuit merchant services, let’s cover one crucial caveat: For your business to access any version of QuickBooks Payments or POS, it will need an account with the corresponding version of QuickBooks accounting software.

You’ll need a QuickBooks Online account to access QuickBooks Online Payments, and you’ll need a QuickBooks Desktop account to access either of the two QuickBooks Desktop Payments or the POS interface.

Basically, QuickBooks merchant services will function much like an add-on to Intuit QuickBooks accounting software. So, if you’re using an accounting software other than QuickBooks Online or Desktop — and you’re fully attached to your accounting software — then you’ll have to look beyond Intuit merchant services for your payment processing solution.

Intuit merchant services overview

No matter which of the following three versions of QuickBooks merchant services you end up choosing for your business, you'll have access to the Merchant Center Intuit created for their small-business customers.

Plus, every transaction you run through Intuit merchant services will automatically store and sync in your accounting software. Because this feature can save business owners so much tedious bookkeeping, the automatic sync is one of the biggest draws that QuickBooks Payments offers.

Finally, though each version of Intuit merchant services offers different types of payment processing, each will allow your business to process at least three types of payments.

Beyond payment processing, automatic bookkeeping, and the Merchant Center, Intuit merchant services products differ depending on which version your business ends up choosing.

Here's a QuickBooks tutorial about connecting card readers, which may provide a helpful look at the interface and features.

Intuit merchant services payment summary

Intuit Merchant Services Product

Price Per Month

Bank Transfer (ACH)

Card (Swiped)

Card (Invoiced)

Card (Keyed)

QuickBooks Online Payments



2.4% + $0.25

2.9% + $0.25

3.4% + $0.25

QuickBooks Desktop (Pay as You Go)



2.4% + $0.30

3.5% + $0.30

3.5% + $0.30

QuickBooks Desktop (Pay Monthly)



1.6% + $0.30

3.3% + $0.30

3.3% + $0.30

Note that none of these payment plans comes with a long-term contract or early termination fee. Simply pay as you go and cancel at any time.

Intuit merchant services options

You know what they cost. Now let's see what each one can do for your small business.

1. QuickBooks Online Payments

The first of your Intuit merchant services versions to choose from is QuickBooks Online Payments.

This QuickBooks merchant services product allows for free bank transfer payments, along with lower payment processing fees for card payments. Plus, you won’t have to pay a monthly fee in order to access these lower payment processing fees.

You’ll also be able to access the online Merchant Center that Intuit tailors specifically to your business based on your QuickBooks accounting software and QuickBooks Payments accounts.

All in all, QuickBooks Online accounting software users hoping for Intuit merchant services are in luck with QuickBooks Online Payments. And those looking for Intuit merchant services — but who aren’t yet QuickBooks Online accounting software users — might consider opening an account for both of these services.

Quickbooks Online

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on QuickBooks' website

2. QuickBooks Desktop Payments (Pay as you go)

On the other hand, if your business is using a version of Intuit QuickBooks Desktop as its accounting software, then you’ll have access to Intuit merchant services through QuickBooks Desktop Payments.

Just like the online version of Intuit merchant services, the desktop version will allow your business access to the Merchant Center Intuit designs for it, payment processing capabilities and automatic sync with accounting software.

Unlike the online version of QuickBooks merchant services, this desktop version has two different payment structures.

The first version of QuickBooks Desktop Payments is the “Pay as You Go” version. This version of Intuit merchant services will allow your business to pay piecemeal through a slightly higher payment processing fee.

3. QuickBooks Desktop Payments (Pay monthly)

Alternatively, if your business uses QuickBooks Desktop accounting software, but processes a high volume of payments, then the monthly plan for the desktop version of Intuit merchant services might be a better fit.

With the monthly plan for QuickBooks Desktop Payments, your business will pay $20 per month in order to access a smaller payment processing fee for every transaction it runs through QuickBooks merchant services.

Again, you’ll still gain access to payment processing, accounting software sync, and the Merchant Center — Intuit QuickBooks Desktop Payments “Pay Monthly” version will only differ from the “Pay as You Go” Online version in the way your business pays for it.

Intuit merchant services additional payment options

On top of Intuit merchant services' more traditional payment options, there are a couple of unique payments products that some small business owners may find useful. We'll go over them here:

1. GoPayment

GoPayment is a mobile app by Intuit that connects with a card reader via Bluetooth to process payments. This is an ideal option for merchants who want to sell on the go. Furthermore, when you sign up for GoPayment you will receive a free mobile card reader from Intuit that can accept magstripe and chip credit cards. GoPayment also syncs with your QuickBooks Online or Desktop account, for easy bookkeeping.

There is no monthly fee to use GoPayment. In-person payments cost 2.4% + $0.25 per transactions, and "card not present" transactions cost 3.4% + $0.25.

2. QuickBooks Ecommerce

QuickBooks Ecommerce is a payment gateway that connects with a handful of major e-commerce platforms, including Shopify and BigCommerce, to allow you to process online payments. QuickBooks Ecommerce comes with SSL encryption and fraud prevention services and also records all transactions in your QuickBooks accounting software.

The price of QuickBooks Ecommerce is the same as the price for QuickBooks Desktop Payments: 2.4% + $0.30 if you pay as you go, and 1.6% + $0.30 if you pay a base fee of $20 per month.

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Intuit merchant services POS software

If you’re not content with payment processing, accounting software and access to the Merchant Center, we recommend looking into QuickBook's POS software.

If you’re used to all things QuickBooks Desktop, check out QuickBooks Desktop POS software to accompany your QuickBooks merchant services. And just like QuickBooks Payments, with QuickBooks POS software, you’ll have options to choose from.

That said, be sure to keep in mind that none of these QuickBooks POS software options come with any kind of hardware included. So, in order for your business’s POS to function fully, you’ll have to make some separate hardware purchases.

Not to mention, QuickBooks POS software will only be able to sync with QuickBooks Desktop financial software, so QuickBooks Online Payments and accounting software users will be out of luck.

QuickBooks Desktop users will want to know if QuickBooks POS software is an upgrade worth pursuing. As such, let’s take a beat to consider all three of your QuickBooks POS software options to see if they’re just the step up you want for your Intuit merchant services:

1. QuickBooks Basic POS

The most affordable version of QuickBooks POS software is the Basic plan.

QuickBooks Basic POS will cost your business a one-off sum that starts at $1,200. With the Basic QuickBooks POS software, you’ll be able to:

  • Ring sales.

  • Take payments.

  • Keep track of customer data.

  • Perform basic reporting.

2. QuickBooks Pro POS

Your mid-level option for QuickBooks POS software is the Pro plan. This plan — which will cost your business a lump-sum rate starting at $1,700 — comes with all of the capabilities of the Basic plan, plus:

  • Manage inventory.

  • Employee management.

  • Payroll.

  • Layaway capabilities.

  • Gift cards capabilities.

  • Rewards and loyalty programs.

  • Advanced reporting.

3. QuickBooks Multi-Store POS

The most powerful version of QuickBooks POS software you could choose from Intuit merchant services is the Multi-Store plan. Unsurprisingly, the Multi-Store plan is also the most expensive version of this POS software — its one-off price starts at $1,900.

That said, for that higher price, the Multi-Store plan will augment your Intuit merchant services with the following capabilities beyond those of the Pro plan:

  • Manage multiple stores.

  • Track inventory.

  • Transfer inventory.

  • Advanced sales reporting between stores.

  • Advanced inventory reporting between stores.

Intuit merchant services hardware

Intuit sells a variety of POS hardware pieces. The products and prices are as follows:

QuickBooks POS Hardware

What It Costs

EMV Ready PIN Pad


Receipt Printer


Barcode Scanner


Wireless Barcode Scanner


Cash Drawer


Pole Display


Tag Printer


If you purchase your products through the Intuit website, a representative will help you craft the POS hardware kit that makes the most sense for your business.

Intuit merchant services alternatives

Now that you’re familiar with all the ins and outs of Intuit merchant services, it’s time to take a step back and consider your next steps.

From here, your next move will depend on how you feel about all you’ve learned about QuickBooks merchant services. If you need more payment processing and accounting software syncing, Intuit merchant services simply might not be the best choice for your business. Plus, attaching QuickBooks POS software to your Intuit merchant services might be either too costly for smaller businesses, or simply impossible for QuickBooks Online users.

If you’re thinking twice about Intuit merchant services, then take a look at these alternatives:

Square POS

One of the best alternatives to Intuit merchant services is Square POS systems.

Unlike Intuit merchant services, Square POS systems are customizable and fully integrated. They’ll allow your business to either convert a smart device into a powerful point of sale, or invest in an all-in-one point of sale, complete with payment processing capabilities, point-of-sale software and point-of-sale hardware.

Plus, Square offers some of the most affordable POS options on the market — with free hardware and a free software option, the only unavoidable cost with Square will be a payment processing fee.

And unless you manually key in card payment, this processing fee will only cost you 2.6% + $0.10 of the transaction value.

Square POS

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on Square's website

Clover POS

Another top alternative to Intuit merchant services for you to consider is Clover POS systems.

Just like Square, Clover offers fully integrated POS systems that allow you to access payment processing, point of sale hardware and point of sale software, all in one bundle.

Unlike Square though, most of Clover’s POS systems won’t require you to have or invest in a smart device.

In fact, only one piece of Clover POS hardware — Clover Go — will connect to a smart device. The four other POS systems that Clover offers come complete not only with fully functioning hardware and software but also with barcode scanning and receipt printing capabilities.


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on Clover's website

Are Intuit merchant services right for your business?

After learning all the ins and outs of Quickbooks merchant services, you’re in a good position to answer this question for yourself and your business.

The way we see it, despite all it has to offer — including payment processing, accounting software syncing and access to the Merchant Center — Intuit merchant services could very well not be the right fit for your business. This is a remarkably narrow product and can basically only serve existing Intuit customers. If that’s nog you, or if you need an inclusive payment processing solution, keep shopping for other options.

This article originally appeared on Fundera, a subsidiary of NerdWallet.

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