QuickBooks Online vs PayJunction

FreshBooks

Stripe

QuickBooks Desktop

Wave

PayPal Checkout

ddSuite

Compare QuickBooks Online and PayJunction based on features, pricing, verified reviews, integrations & more on GetApp. Find out which software is best for your business in 2026.

FreshBooks is accounting software that helps small business perform accounting tasks, conduct invoicing, manage expenses, and more.

Wave is an integrated solution designed for small businesses. With our automatic bank connections, information flows into Wave, without manual entry. Users can collaborate with accountants or bookkeepers in real-time.

QuickBooks Desktop provides a comprehensive business management solution that integrates accounting, payroll, inventory, and multiple company management functionalities. The software offers industry-specific editions tailored for manufacturing, wholesale, contractors, and accountants, with features like advanced reporting, job costing, and automated pricing rules. Users can enhance their experience with cloud hosting capabilities that enable remote access and team collaboration.

QuickBooks Online is an all-in-one online business software designed to help manage business finances. The platform is built to scale businesses, unlocking insights and providing the functionality of a larger team, all on one integrated platform.

"What If" Scenarios

1099 Preparation

401(k) Tracking

Accounting

Accounts Payable

Accounts Receivable

Accrual Accounting

ACH Payment Processing

Activity Dashboard

Activity Tracking

Ad hoc Reporting

Address Validation

Aging Tracking

Approval Process Control

Asset Accounting

Asset Lifecycle Management

Asset Tracking

Attendance Management

Audit Trail

Automatic Backup

Automatic Billing

Bank Reconciliation

Benefits Management

Billable Items Tracking

Billing & Invoicing

Billing Portal

Budgeting/Forecasting

Cash Flow Management

Cash Management

Categorization/Grouping

Chart of Accounts

Check Printing

Check Processing

Check Writing

Client Management

Commission Management

Compliance Management

Consolidation/Roll-Up

Consumer Use Tax

Contact Database

Contingency Billing

Core Accounting

Cost Estimating

Cost Management

Credit Card Management

Credit Card Processing

Cross Ledger Posting

Customer Accounts

Customer Statements

Customizable Branding

Customizable Fields

Customizable Forms

Customizable Invoices

Customizable Reports

Customizable Templates

Dashboard

Data Import/Export

Data Visualization

Direct Deposit

Discount Management

Document Templates

Donation Management

Donation Tracking

Donor Management

Drag & Drop

Dunning Management

Duplicate Payment Alert

Electronic Funds Transfer

Electronic Payments

Electronic Signature

Email Management

Employee Management

Estimating

Exemption Management

Expense Claims

Expense Management

Expense Tracking

Fee Calculation & Posting

Financial Aid Management

Financial Analysis

Financial Management

Financial Reporting

Fixed Asset Management

For AEC Industry

For Higher Education

For Medical Purposes

For Nonprofits

For Real Estate

For Religious Organizations

For Small Businesses

For Trucking Industry

Forecasting

Fraud Detection

Fund Accounting

Fund Management

General Ledger

Grant Management

Hourly Billing

QuickBooks Online

Android

Web-based

Windows

iPad

iPhone

Business banker 

It's a user friendly service with great customer care, wonderful service if u have a small business.

Owner

This is extremely unprofessional and unacceptable from the company that is supposed to have your books.

Accountant

Fields to fill and perfectly links the data from one end like ap and AR to the bank reconciliation. Great reports on transactions for the month or period if interest.

Admin

We love that it helps us streamline efforts, is easy to use, and is easy to train others on. QuickBooks Online has definitely been one of the best technology pieces of our administration.

Finance and Accounting Lead

This software has a lot of great features, the best of them all is the ability to import data from.

OWNER

Quickbooks Online has a lot of wonderful features that are super easy to use and deploy in the office. A lot of time is saved with repetitive tasks that eat up a already busy day.

Principal/Manager

Love that it is cloud-based and can login from anywhere. I love that myself and my team can all be working in the same company file at the same time from wherever we are.

Accountant 

Quickbooks online is super easy to use, offers lots of features and can supports many users. The interface looks amazing.

Inside Sales Representative

The problem is that doing your own taxes online becomes risky the more you have to account for.

The ease of integration with our financial institution was outstanding. The amount of time that will be saved on preparing taxes documents is such a blessing.

Manager

Not only that but its very intuitive, and simple. I love the help button and search bar which can help you find almost anything.

Account Specialist

The ease of use has to be at the top of the list. It is an amazing software to help us keep track of 7 companies.

Accounting Assistant

Fantastic, the customer service team is always available to help if you have any issues.

What I like most about QuickBooks is that it tracks all my expenses. It also tells me what I spent on my savings account and how to save money.

We love the ease of reporting in Quickbooks online and how easily it integrates with our other systems.

Office Manager

Other than tracking my expenditures, the whole system is a pain. Error messages constantly received because "there's a message from your bank" bla bla bla.

They have the among the worst support I have ever dealt with.

Content Creator

Quickbooks is perfect for small businesses who need to track their own expenses to save on costs. It seriously offers so many features and is really everything you will need to manage your expenses.

QuickBooks Online screenshot: QuickBooks Online dashboard

QuickBooks Online screenshot: QuickBooks Online analytics

QuickBooks Online screenshot: QuickBooks Online transactions

QuickBooks Online screenshot: QuickBooks Online invoice

QuickBooks Online screenshot: QuickBooks Online customers and leads

QuickBooks Online screenshot: QuickBooks Online expenses

QuickBooks Online screenshot: QuickBooks Online marketing

QuickBooks Online screenshot: QuickBooks Online reporting

QuickBooks Online screenshot: QuickBooks Online taxes

QuickBooks Online screenshot: QuickBooks Online apps

Freelancers

Large Enterprises

Mid Size Business

Non Profit

Public Administrations

Small Business

Stripe is a comprehensive financial infrastructure platform that enables businesses to accept payments online and in person. It offers a suite of APIs for payment processing, subscription management, fraud prevention, and financial services integration, supporting over one hundred payment methods across multiple currencies. Stripe provides both developer-focused tools with extensive documentation and no-code solutions for businesses without technical staff.

PayPal Checkout is a payment checkout platform that enables retailers to process payments via various payment modes.

ddSuite software from DDC Schweiz allows object data of large infrastructure objects to be viewed from the overall view down to the smallest detail, managed and orders and invoices to be triggered.

PayJunction is a payment gateway & merchant service which provides mid to large scale enterprises with the tools to process all payment types in store or online

Customer History

Debit/Credit Card Processing

In-Person Payments

Mobile Payments

Multi-Location

Online Payments

Payment Gateway Integration

Payment Links

Payment Processing

PCI Compliance

Point of Sale (POS)

Projections

Receipt Management

Recurring/Subscription Billing

Reporting/Analytics

Sales Reports

Search/Filter

Status Tracking

Third-Party Integrations

Transaction History

Transaction Monitoring

PayJunction

Admin Assistant

This is very user friendly and if we experience any difficulties we just call and someone is very helpful to assist in problem solving. Everyone has been very supportive and is very helpful.

Billing Manager

It is a great product and they do a great job supporting it. The staff are friendly and professional and always resolve my problems quickly.

President

Support - they are friendly and available when they are needed. I love the kiosk that is provided - we've received numerous compliments about how easy it is to use, and how fast it is.

Operate my own business--owner

I am responsible for managing associations and we had to find a very good company at a good price point. We found Pay Junction and it fitted our needs very well.

PayJunction has been a super convenient and helpful solution with instantaneous access to customer profiles and capture data.

Finance Manager

We have been using it for quite a number of years and it has really helped our business. Would recommend to anyone looking for a wonderful credit card/check processing company.

QuickBooks Online vs PayJunction Comparison (2026)

QuickBooks Online vs PayJunction Comparison (2026)

QuickBooks Online

PayJunction

Overview

Video & Screenshots

Pricing

User reviews

Key features

Integrations

Alternatives