Top 4 QuickBooks Payments Alternatives
Kyle Kuczynski
Kyle Kuczynski
MessageDesk Co-Founder & CMO
Updated: Jul 31, 2021
QuickBooks Payments Alternatives

Looking for a QuickBooks Payments Alternative? Here Are 4 Options and Several Things to Consider

In the world of accounting and payments, 62% of small businesses use QuickBooks worldwide. That equates to over two million customers.

But having the right invoicing software or payments system is just one part of running a cashless business and getting paid faster and on time.

In a recent survey of 400 businesses, 27% noted that they have a hard time creating and sending invoices. Another 46% said they have difficulty getting paid on time. While 49% said they have a hard time following up on late payments.

Even though many businesses use QuickBooks Online and QuickBooks payment processing to accept credit card payments and create transactions, QuickBooks Payments fees can make a hard thing even harder. This is especially true for those who just need a faster, simpler way to get paid on time.

The good news is we’ve got a list of several alternatives to QuickBooks payments. Read on for more.

What is QuickBooks Online Payments?

QuickBooks Payments makes it possible for small businesses to accept credit card payments and get paid online. You can use a multitude of payment methods including debit card, credit card, Apple Pay, phone order, or bank transfer. The best part is that managing payment, credit card transactions, and invoicing all get done in one place.

If you use QuickBooks for bookkeeping, then QuickBooks Payments is a great way to simplify cash flow and payments with features like customizable invoice templates and more. But, not everyone uses QuickBooks Payments and some want alternatives, especially when it comes to fees.

QuickBooks Online Payments Fees:

If you use QuickBooks Payments then you’re already paying:

  • 2.9% and $0.25 per transaction with no monthly fees
  • Or 2.75% and $0.25 per transaction with $16 in monthly costs

Regardless of which option you choose, you’ll need to sign up for or have an existing QuickBooks Online account before accepting payments.

Suggested Article: Ultimate Guide to QuickBooks Online Invoicing

Free QuickBooks Payments Alternatives

Unfortunately, there are no QuickBooks Payments alternatives that are completely free. But there are other paid alternatives to QuickBooks Payments that work well for small businesses.

Keep in mind that many of these options do come with processing fees.

The Top 4 Best QuickBooks Online Payments Alternatives in 2021 (In No Particular Order)

  1. MessageDesk
  2. Xero Payments
  3. Square Payments
  4. PayPal Invoicing

1. MessageDesk Payments (powered by Sphere)

MessageDesk Logo.png

MessageDesks Payments is a great way to receive payments from customers.

You can send invoices via text to your customers and get paid on the go. MessageDesk helps you send texts with links that make it easy to receive payments in QuickBooks.

Since texts are read 98% of the time text-to-pay is arguably the most effective payments options for getting paid faster.


  • Automatic payment reminders
  • Automatic past due reminders
  • Text-to-Pay features
  • Integrates with QuickBooks and Xero to enable text-to-pay


  • No accounting features
  • No way to email invoices


Processing Fees:

  • 2.85% + $0.25 per transaction

What customers have to say:

"This has been a great tool helping us to text our owners and keep the lines of communication open while not keeping our front desk on the phone constantly." - Review from Capterra

"This allows our customers to directly connect with us without having to remember another phone number. Most of our customers are on the go and love to get texts rather than read an email." - Review from Capterra

“This has been the app that I have been looking for and researching for over a year. I have had several trials with other software but those seem to be geared toward the big businesses. We are a small company with a small budget. I feel like this software and our needs are the perfect pairing. I wish I would have found them much earlier.” - Review from Capterra

2. Xero Payments

Xero Logo.png

Xero is a New Zealand based accounting platform that specializes in small business accounting.

They’re a direct competitor with QuickBooks online and offer one of the best alternatives to QuickBooks Online Payments. Invoicing also comes as a part of their accounting software.



  • Uses a third party (Stripe) for their payment processing
  • Monthly cost on top of processing fees


  • $11 per month to send 20 invoices a month.
  • $32 per month to send unlimited invoices a month.

Processing Fees:

  • 2.9% + 30 cents per transaction (based on Stripe Prices)

What customers have to say:

“Great, easy to use, and saves a lot of bookkeeping time. presentation of invoices and receipts to customers is professional and simplified payment systems mean they can pay without any barriers. More than one customer in an account would be a massive improvement.” - from Software Advice

“Xero is easy to use and very mobile, the only thing that would make it better is being able to take credit card payments. I do use Stripe but it can be difficult to reconcile.” - from Software Advice

3. Square Payments

Square Logo.png

Square invoicing is just one part of Square’s payments platform that goes as far as having a physical card reader. You can configure their platform depending on the type of industry you’re in.

Square’s payments and invoicing are free but their processing fees are considerable.


  • Easy to set up
  • No monthly cost
  • Simple software


  • High processing fees


  • Free

Processing Fees:

What customers have to say:

"It's ease of use is amazing. Everything is very easy to understand and the software is very user-friendly." - from Capterra

“My only hang-up with Square is their high processing rates. I'm aware that they can offer better rates if a business does greater than $250k annually in sales, but that's only if the payments have all been through Square. So it's a little annoying that we're easily surpassing that and proving that with previous years' reports is not sufficient.” - from Capterra

"I dislike the fees that are charged for people processing payments for each transaction." - from Capterra

4. [PayPal Invoicing]

PayPal Logo.png

PayPal provides a seamless invoicing experience. The only downside is limited customization.

Similar to Square, with no monthly cost comes high processing fees. This can turn away many business owners depending on the volume of payments they complete in a given month.


  • No monthly cost
  • Easy to use


  • High processing fees
  • Limited customization of invoices



Processing Fees:

What customers have to say:

"The fees, the fees, the fees. With PayPal, they charge you for so many things, it gets a little ridiculous." - from Capterra

"I love Paypal and I love their invoicing services, I use them pretty much every day and sometimes multiple times a day and it's for sure the only invoicing platform that I like to use." - from Capterra

Ready to meet with a payments expert?

MessageDesk can help you get paid faster with text-to-pay, payment reminders, and past due reminders.

Seamlessly integrate with Quickbooks Online, Xero, or use MessageDesk’s native invoicing powered by Sphere.

You can always Try for free, but feel free to schedule a demo.

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