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PayJunction vs Square Payments

Updated February 9, 2026

PayJunction vs Square Payments: Which is best for you?

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55+ software advisors
1 million+ businesses helped
2 million+ verified software reviews
Starting Price
$50.00

one time

Pricing available upon request

Free Trial
Free Version
Screenshots
and Demo
Product Screenshot
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Product Screenshot
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Top Rated
  Features
Online Payments
5.0
Mobile Payments
5.0
Debit/Credit Card Processing
4.88
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Transaction History
4.92
Receipt Management
4.88
Credit Card Processing
4.79
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Integrations
Shift4Shop
Shift4Shop
Shopify
Shopify
Adobe Commerce
Adobe Commerce
See All
Zoho Invoice
Zoho Invoice
Wix
Wix
Ecwid
Ecwid
See All
Pros / Cons
  • Althought the rates are higher, we do feel the efficiency and accuracy of payment collection is more than worth it.
  • PayJunction costs a monthly fee and when I wasn't using it much, that was a difficult expense to justify.
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  • Overall, Square Payments is a very good payment-processing solution for small-to-mid sized businesses, startups, side hustles, or anyone who values ease of setup and flexibility over deep customization or maximum cost efficiency.
  • The flat percentage-per-transaction model can be more expensive than custom merchant-account rates if you do a lot of sales, or have large-ticket items — so for high-volume businesses, fees may become significant.
Read more
Ease-of-Use
Highest performing feature
in the comparison
4.8/ 5
4.7/ 5
Value for Money
4.5/ 5
4.5/ 5
Customer Support
Highest performing feature
in the comparison
4.7/ 5
4.4/ 5
Functionality
Highest performing feature
in the comparison
4.7/ 5
4.6/ 5
Support Options
Email/Help Desk
FAQs/Forum
Knowledge Base
Phone Support
24/7 (Live Rep)
Chat
Email/Help Desk
FAQs/Forum
Knowledge Base
Phone Support
24/7 (Live Rep)
Chat
Training Options
In Person
Live Online
Webinars
Documentation
Videos
In Person
Live Online
Webinars
Documentation
Videos
FrontRunners
N/A
FrontRunners 2026
Advisor
  Recommendations
N/A
N/A
Ideal Customer Size
Small
Medium
Large
Small
Medium
Large
Deployment Options
Cloud, SaaS, Web-Based
Desktop - Mac
Desktop - Windows
Desktop - Linux
Desktop - Chromebook
On-Premise - Windows
On-Premise - Linux
Mobile - Android
Mobile - iPhone
Mobile - iPad
Cloud, SaaS, Web-Based
Desktop - Mac
Desktop - Windows
Desktop - Linux
Desktop - Chromebook
On-Premise - Windows
On-Premise - Linux
Mobile - Android
Mobile - iPhone
Mobile - iPad