Payments on QuickBooks: What Are My Options?

Learn about options for payments on QuickBooks, plan pricing, QuickBooks payments fees, benefits of accepting payments through QuickBooks & more!

When you’re starting a business, staying on top of company finances can seem like a huge stressor. Something that's impossible to tackle on your own.

For many, QuickBooks is a solution to this problem. This software from Intuit he Intuit software has gained a strong reputation among business owners, particularly for its simple electronic invoicing tools. However, that’s not the only payments option that QuickBooks offers.

In this article, we’ll briefly cover the payment options offered by QuickBooks. That includes software pricing, QuickBooks merchant services fees, and the costs relative to a more traditional payments system.

Do you need a better payment processing solution for your business? Swipesum’s independent payments consultants are here to help with free guidance, advice, and negotiation support.

Our team can help you find the best solution for your unique needs. They’ll also identify opportunities to eliminate fees related to accepting payments. Book your free consultation now!

Options for Payments on QuickBooks

QuickBooks is well-known for it's great invoicing capabilities. However, there are a number of other ways that business owners can process payments through the software. Here are a few of the possibilities:

Online payments:

Through QuickBooks, you can add a “Pay Now” button to your company’s website. That makes it easy to accept payments via credit card, debit card, Apple Pay, or an ACH bank transfer According to Intuit, QuickBooks processing fees for online payments include:

  • QuickBooks ACH fees: 1%, up to a maximum of $10

Recurring payments:

If you run a subscription service or charge regular membership fees, QuickBooks enables you to set up automatic payment plans. You can use any of the payment methods listed above.

There is no additional QuickBooks online payment processing fee or other cost for recurring payments.

On-the-go payments:

Do you need to accept in-person payments along with your website options? QuickBooks can provide you with a physical card reader.

All of the payments processed through the Bluetooth reader appear automatically inyour QuickBooks GoPayment app. That makes logging these transactions a cinch. You can also purchase more card readers that range from $19-$49, depending on what features your business requires. QuickBooks credit card payment fees through a physical reader will cost you 2.4% plus $0.25.

Over the phone:

Does your business only accept cards in this rarest of circumstances? QuickBooks allows you to enter your customer's card information into the software to process payments.

You’ll see higher QuickBooks payment processing fees in this case, but it’s not a bad option for one-off card transactions. Because of the increased risk of these transactions, QuickBooks charges 3.4% plus $0.25 per keyed-in transaction.

Digital invoicing:

This is perhaps QuickBooks greatest strength, QuickBooks invoice fees on digital invoices incur a charge of 2.9% plus $0.25 per transaction. If customers elect to use an ACH payment, there is no charge.

NOTE: All the above pricing is for the QuickBooks Online membership. Business owners who invest in QuickBooks Desktop will see reduced QuickBooks merchant services rates.

For all of the payment options, QuickBooks authorizes the individual payments that are then batched once a day. After one or two business days, those funds will appear in your company’s account.

Although transactions will automatically be saved in your software, you won’t receive the funds until a few days afterward.

A person uses a credit card to make a payment with their laptop computer.

QuickBooks Plan Pricing

For new users, QuickBooks offers a 30-day free trial. Once that blissful period is over, you have to choose a payment plan to keep your account running.

The cost of the software is really dependent on your business’s unique needs, but there are generally three options to choose from. Each has their own payment costs.


This service has no monthly fees, but rather charges “as you go.” Depending on the payment method, per-transaction fees range from 2.4 to 3.4% plus $0.25.

Unless you rarely accept card payments, this option should be avoided at all costs. The percentages of these merchant account fees are exorbitantly high. That’s true, even when compared to the QuickBooks desktop version.


With QuickBooks Desktop, you can choose to either follow the “pay as you go” plan or to pay a $20 fee with lower per-transaction fees.

Per-transaction fees range from 1.6% to 3.3% plus $0.30 on this tier. Both QuickBooks Desktop and QuickBooks Online charge an additional $1 for each ACH payment. This is where your numbers come into play to decide which option will save you from paying extra for fees.

Pre-set plans:

QuickBooks also offers a handful of pre-set plans for specific businesses.

These include three “Small Business” options—”Simple Start,” “Essential,” and “Plus”—that charge monthly fees ranging from $20–$60 (plus per-transactions fees) per month. Each tier offers various special features tailored to the business type.

QuickBooks also offers a “Freelancer” option for $10/month (plus per-transaction fees). The software also provides an “Advanced” version for $150/month.

Benefits of Accepting Payments Through QuickBooks

QuickBooks is a good option for small businesses who don’t have the time or expertise to set up their own accounting systems. The software is intuitive, and all of your transactions end up neatly in the same place in real time.

It also offers a variety of payment methods. That makes it easier for your customers to pay you, whether it’s a one-time payment or recurring. Knowing you can accept a variety of payments makes day-to-day operations that much easier.

QuickBooks also reconciles matched invoices and payments automatically. That means you have a better chance of getting your money in a timely manner. It’s another way that QuickBooks can help make your business run a little smoother.

Finally, you know what you’re getting into cost wise when you set up the account. All of the numbers for the different options are on the website for your perusal. QuickBooks has a lot to offer, but the costs might not align with your company’s needs. And there are plenty of other options out there.

Possible Issues with QuickBooks Payments

The benefits of QuickBooks might sound promising — and they are. However, that’s not the only thing to consider.

There's not really anything on offer here that can't be found in other accounting software. Like most “all-in-one” or “one-size-fits-all” software, there are a few drawbacks. That’s true especially when it comes to payments.

If you're concerned about the high cost that comes with accepting payments through QuickBooks, you’re not alone. It’s a significant issue for a wide variety of businesses.

In search of a more affordable option that can deliver many of the same benefits? We recommend seeking out an alternative that allows external payment integrations, such as Xero. These will offer similar services with more flexibility to find a payments option that works for your business.

Simply stated: businesses that use QuickBooks to accept card payments are locking themselves into an overpriced contract. Yes, the software is sleek and effective, but it's certainly not the most cost-effective way to take payments.

Looking for the best possible payment processing solution for your business? Swipesum is dedicated to helping companies just like yours make payments more efficient, less costly, and easier to manage.

Our team can help you source the best payment solution for your unique position and needs. We’ll help with everything from identifying potential providers to negotiating for the best rates.

Request your free consultation today!

Taft Anderson

Taft Anderson

Taft Anderson is the former Product Marketing Manager of Swipesum. A graduate of Washington University in St. Louis' Olin Business School, Taft is a content and branding expert.

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