Credit Card Processing

FreshBooks vs. Intuit GoPayment and QuickBooks for Taking Credit Cards

by Ben Dwyer

Accounting software company FreshBooks is a popular choice, but how does it compare to behemoth Intuit when taking credit cards?

In the past, FreshBooks offered its own mobile reader. A benefit is that it integrated directly with the accounting software. However, the company no longer offers its own reader, which removes that advantage. That leaves competitor Intuit GoPayment, the mobile processing solution from the makers of QuickBooks. How do FreshBooks and Intuit’s GoPayment mobile processing options compare?


One downside to both FreshBooks and Intuit GoPayment is the cost to process cards. Neither option uses interchange plus pricing, meaning both can be more expensive than what you could be paying with competitive interchange plus. There are exceptions: businesses with small average transactions (under approximately $10) or those that only process a few thousand dollars per month will likely find flat rate pricing like FreshBooks to be reasonably priced compared to other options.

FreshBooks GoPayment (pay-as-you-go) GoPayment (monthly)

Visa and Mastercard:
2.9% + $0.30 per transaction

American Express:
3.5% + $0.30 per transaction

2.5% per transaction

3.5% per transaction

Monthly fee: $19.95

1.6% + $0.25 per transaction

3.2% + $0.25 per transaction


FreshBooks utilizes a flat-rate pricing structure, similar to Square. Even ignoring the fact that you can likely get lower cost mobile processing with an interchange plus model offered by processors (including credit card processing companies that place quotes through CardFellow) the pricing noted above makes FreshBooks a bit more expensive than Square, PayPal Here, and other mobile solutions like the Clover Go. Additionally, it doesn’t offer its own readers anymore, so you’ll need to purchase equipment from a third party.


Intuit GoPayment has previously used tiered pricing models, leading to opaque and expensive processing. The company now appears to offer a flat-rate structure, and doesn’t reference qualified, mid-qualified, or non-qualified transactions in their pricing disclosure. Currently, the company’s pricing page lists just percentage rates with no per-transaction fees. That is somewhat uncommon.

One possible explanation surfaces in the fine print of Intuit’s pricing disclosure, which states, “All fees stated in this Pricing Schedule are fees that Intuit charges you and are not fees charged to you directly by the card and payment networks.” It’s possible that Intuit’s published rates are on top of the wholesale costs of processing (that is, the interchange and assessment costs from banks and card brands) but this is not readily confirmed by Intuit, and would be a very expensive markup. Bottom line: We’re credit card processing experts and even we have difficulty figuring out exactly what Intuit is charging. It doesn’t inspire a lot of confidence that Intuit can’t provide clear and direct information on their pricing, which should make anyone suspicious, especially given Intuit’s expensive pricing history.

Winner: FreshBooks due to greater transparency and the likelihood of costing less than GoPayment once Intuit’s extra fees are factored in, but neither are particularly competitive options.


In the past, both companies offered an EMV-compatible reader, but these days, only Intuit does. With the EMV readers, you’ll be able to take both traditional magnetic stripe credit cards and the new EMV chip cards.

FreshBooks EMV reader Intuit GoPayment EMV reader
                Available: No Yes
                Cost: N/A $49
                Compatibility: N/A Apple and Android devices

Winner: Intuit GoPayment, by default. FreshBooks no longer offers its own reader.

Settlement Time

For deposits, FreshBooks and Intuit GoPayment offer fairly similar timeframes.

                                   FreshBooks                     Intuit GoPayment
                                   2-5 business days                      1-5 business days

Winner: Intuit GoPayment, because of the possibility of 1 day funding although it’s likely to take longer.

So who should I go with for mobile processing, FreshBooks or GoPayment?

In our opinion: It depends. FreshBooks is our suggestion if your business fits the profile likely to benefit from flat rate pricing. (Roughly, if you’re processing less than about $3,000/month in cards, or if your average transaction is less than about $10.)

In any event, we can’t in good conscience recommend Intuit GoPayment even if its reader is compatible with more devices and has the possibility of faster funding, simply because its pricing and practices have historically been deceptive and expensive. We haven’t seen anything to indicate that has changed with GoPayment, though we’re willing to be proven wrong.

FreshBooks, while more transparent, is still an expensive option for mobile outside of the conditions noted above. If mobile processing is a priority for your business, but you process a lot of card volume or have higher transaction totals, it’s worth your time to check out the mobile solutions available from processors that offer more competitive interchange plus pricing.

How are FreshBooks mobile and Intuit GoPayment different than Square?

The main difference is that FreshBooks mobile and Intuit GoPayment are both from accounting software companies and are designed to seamlessly integrate with those accounting programs. FreshBooks mobile processing integrates directly with FreshBooks cloud accounting, while Intuit GoPayment integrates with QuickBooks. For businesses that use those programs, there’s a lot of appeal to everything connecting easily.

However, Intuit does partner with Square. If you use Square and QuickBooks, Intuit’s partnership will allow you to easily integrate your Square transactions with your QuickBooks account.

Can I use the readers with other processors?

No. You can still use FreshBooks or QuickBooks accounting software and take credit card payments through another processor, but to use the GoPayment reader you’ll need to process with Intuit Payments.

If you’re looking for a mobile processor and don’t want to use FreshBooks or GoPayment, you can view more options with free quotes through the CardFellow credit card processing marketplace. Accounts are free, private, and only take a few minutes to set up. You can still use QuickBooks or FreshBooks accounting programs with other processors, so you get the best of both worlds: competitively priced credit card processing (even by smartphone) and the ability to keep your favorite accounting program. Sign up today.

1 thought on “FreshBooks vs. Intuit GoPayment and QuickBooks for Taking Credit Cards”

  1. I have been using Slickpie for a year now, after switching from Quickbook. So easy to use, I no longer need to outsource bookkeeping services. Multiple options to manage invoices and cash flow. It’s a 100% free accounting software. Fast and easy bank reconciliations.

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