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Top Rated Accounting Software with Payment Processing in 2026

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Verified reviewer profile picture

All user reviews are verified by in-house moderators and provider data by our software research team.  Learn more

Last updated: March 2026

Payment processing in accounting software allows businesses to efficiently manage and track transactions. It supports various payment methods, ensures timely deposits, matches payments to invoices, and integrates with banking systems, improving cash flow and reducing manual entry. Our reviewers in accounting software rated this feature as important.

5 Best Accounting Software with Payment Processing

Product
User rating
Starting price
BQE CORE Suite logo
4.5
(783)
Empty state illustration for "No pricing info"

No pricing info

FreshBooks logo
4.5
(4.5K)
21
flat rate/per month
QuickBooks Enterprise logo
4.5
(20.6K)
2210
flat rate/per year
QuickBooks Online logo
4.3
(8.3K)
38
flat rate/per month
Xero logo
4.4
(3.2K)
25
flat rate/per month

See other top Accounting products with payment processing

How we picked the 5 top rated products

We chose the high-performing solutions on this list based on verified user ratings on our site. Depending on available data, qualifying products either had to be among the most user-reviewed or the most searched-for products in the Accounting software category. They also needed to have sufficient reviews about payment processing, have a minimum user rating of 3 out of 5 for that feature, and show evidence of U.S. market presence. We then added a distinction for up to three products based on our proprietary ratings and reviews: Highest rated, Highly rated for payment processing, and Highly rated for free version. Sponsorship or client status has no influence on the selection of these products, but it may impact the order in which products appear.

Details for the 5 best products

BQE CORE Suite logo
Reviews Sentiment
 
 
 
1-2(36)
3-4(202)
5(545)
Key Features
Income & Balance Sheet4.6
Financial Reporting4.1

User insights about the payment processing feature

Users find BQE CORE Suite's payment processing generally efficient, with the ability to accept credit card and ACH payments. They appreciate the automatic processing of online payments and the ease of tracking payment status. However, some mention issues with error codes and the need for better visibility of outstanding amounts during payment entry.

See related user reviews

“It has allowed us to receive credit card payments and ACH payments, far better then receiving checks. ”
JP

Juan P.

Corporate Development Manager

“Receiving payments in core is a breeze and less time consuming as other programs.”
JC

Jody C.

Financial/Business Manager

Starting price
Empty state illustration for "No pricing info"

No pricing info

Pros and Cons based on 783 verified reviews

Easy to learn

Responsive customer support

Tailored for architects

Comprehensive project management

Slow performance

Frequent bugs and glitches

Delayed issue resolution

See pros and cons details
FreshBooks logo
Reviews Sentiment
 
 
 
1-2(82)
3-4(1,768)
5(2,656)
Key Features
Income & Balance Sheet4.4
Financial Reporting4.5

User insights about the payment processing feature

Reviewers indicate FreshBooks' payment processing is reliable, fast, and easy to use. They appreciate the integration with Stripe and PayPal, allowing clients to pay directly from invoices. Users value the automated payments, secure transactions, and the ability to track payment status. However, some mention issues with delayed deposits and double charging.

See related user reviews

“payment processing is seamlessly integrated into the online invoicing customers can quickly pay their outstanding balance directly from the invoice generated.”
ED

Eugene D.

Project Manager

“FreshBooks integrates with popular payment gateways like Stripe, PayPal, and credit card processors, making it easy for clients to pay directly through invoices. Clients can pay online with just a few clicks, improving convenience and increasing the”
AA

Adah A.

Certified Public Accountant

Starting price
21flat rate /
per month
Pros and Cons based on 4,506 verified reviews

Cloud accounting accessibility

Efficient invoicing capabilities

Tailored for small businesses

Minimal learning curve

Effective freelancer tools

Reliance on internet connection

Limited bank integration

High costs for larger teams

Frequent technical issues

See pros and cons details
QuickBooks Enterprise logo
Reviews Sentiment
 
 
 
1-2(352)
3-4(7,712)
5(12,545)
Key Features
Income & Balance Sheet4.6
Financial Reporting4.6

User insights about the payment processing feature

Users report QuickBooks Enterprise's payment processing is efficient and easy to use, with options for credit card and ACH payments. They appreciate the fast processing times and integration with online payments. However, some find it expensive and mention occasional delays in accessing funds. Reviewers also note the system's reliability and ease of tracking payments.
Verified reviewer profile picture

See related user reviews

“Our Quickbooks is linked with a credit card payment center and posting is done automatically, so we dont have to manually post payments; also this keeps duplicate payments from being made. ”
LB

Linda B.

Bookkeeper

“When a customer pays online using Apple Pay, Google Pay, plus chip and swipe cards, QuickBooks Desktop Payments automatically records and matches the transaction. It further simplifies business”
Verified reviewer profile picture

Ngha N.

Data Analyst

Starting price
2210flat rate /
per year
Pros and Cons based on 20,609 verified reviews
Verified reviewer profile picture

Comprehensive expense tracking

Ideal for small businesses

Effective financial management

Streamlined bookkeeping

Efficient tax management

Frequent issue resolution challenges

Slow performance speed

Disruptive software updates

High cost concerns

Unreliable customer service

See pros and cons details
QuickBooks Online logo
Reviews Sentiment
 
 
 
1-2(456)
3-4(3,151)
5(4,777)
Key Features
Income & Balance Sheet4.5
Financial Reporting4.4

User insights about the payment processing feature

Reviewers appreciate QuickBooks Online's payment processing for its simplicity and reliability. They value the integration with various payment gateways and the ability to accept multiple payment methods. Users note the ease of tracking payments and the convenience of online invoicing. However, some mention high fees and occasional delays in processing payments.

See related user reviews

“It provides smooth connection with a range of payment gateways. This makes it possible for me to effectively receive payments made with bank transfers, credit cards, or other means. For my company, the ease of using QuickBooks' payment processing exp”
MA

Mark A.

Researcher

“I like payment processing in QuickBooks Online because it facilitates timely payments, streamlines financial transactions, improves cash flow management, and enhances overall efficiency.”
AR

Antonio R.

Linguist

Starting price
38flat rate /
per month
Pros and Cons based on 8,384 verified reviews

Cloud-based accessibility

Ideal for small businesses

Seamless integrations

Comprehensive accounting features

Efficient tax management

Frequent bugs and crashes

Limited desktop features

Recurring costs and price increases

Inadequate customer support

Complicated transaction management

See pros and cons details
Xero logo
Reviews Sentiment
 
 
 
1-2(159)
3-4(1,155)
5(1,955)
Key Features
Income & Balance Sheet4.6
Financial Reporting4.4

User insights about the payment processing feature

Reviewers highlight Xero's payment processing as user-friendly and efficient. They appreciate the integration with popular payment gateways like PayPal, Stripe, and GoCardless, which facilitates quick and secure transactions. Users value the automatic linking of payments to invoices and the ease of reconciliation. However, some mention the lack of integration with certain banks.

See related user reviews

“I have integrated my payment processor with Xero and my clients can make payments directly through the invoices I send. This becomes easy for them to view and pay the invoice.”
AA

Abhishek A.

CEO

“Xero integrates with popular payment gateways, allowing users to process payments from their customers quickly and securely.”
DN

Debbie N.

Manager

Starting price
25flat rate /
per month
Pros and Cons based on 3,269 verified reviews

Cloud accounting accessibility

Customizable dashboard

Effective bookkeeping tools

Accessible learning resources

User-friendly interface

Slow issue resolution

Poor customer support

Limited inventory management

Lack of live support

Underdeveloped mobile access

See pros and cons details

Other Top Rated Accounting Software with Payment Processing in 2026

Sage Intacct logo

Sage Intacct

Category Leaders

Best-in-class Cloud ERP for Finance

visit website
Sage Intacct’s core financials automate your most important processes, reduce your reliance on spreadsheets, and give you greater visibility into your business

Read more about Sage Intacct

Users also considered
Zoho Books logo

Zoho Books

Category Leaders

Online accounting software for businesses of all sizes

visit website
Zoho Books helps small businesses to manage all financial activity, from invoices and expenses, to sales and purchase orders, to taxes, reports, and bank feeds.

Read more about Zoho Books

Users also considered
Canopy logo

Canopy

Practice management software for accounting firms

visit website
Canopy is a cloud-based practice management solution for accounting professionals. Streamline your firm and create a connected client experience using our suite of features including workflow, document management, time and billing, payments, a CRM with a secure client portal.

Read more about Canopy

Users also considered
Order.co logo

Order.co

AI-driven procurement and spend management tool

visit website
Order.co simplifies buying for businesses. Eliminate manual purchasing & payment tasks to create one place to purchase, approve, and pay for the products your business needs.

Read more about Order.co

Users also considered
QuickBooks Enterprise logo
Category Leaders

Enterprise accounting, FSM and inventory management solution

QuickBooks Desktop Enterprise is an accounting software for small businesses which provides users with real-time access to customer, employee, and vendor information. The software includes tools for managing inventory, shipping, sales orders, pricing, tasks, invoicing, reporting, and more.

Read more about QuickBooks Enterprise

Users also considered
TaxDome logo

Tax practice management software for bookkeepers and CPAs

TaxDome is a leading practice management platform for tax, bookkeeping and accounting firms, as well as CPAs and EAs. TaxDome allows firms of all sizes to streamline and maintain oversight of their practice by using one platform for both internal practice management and client-facing tools.

Read more about TaxDome

Users also considered
QuickBooks Online logo

Accounting and business management software

QuickBooks Online offers accounting with financial dashboards, invoice creation, online payment acceptance, expenses tracking, payroll & more.

Read more about QuickBooks Online

Users also considered
FreshBooks logo
Category Leaders

Invoice and accounting software tailored to small businesses

FreshBooks automates daily accounting activities namely invoice creation, payment acceptance, expenses tracking, billable time tracking and financial reporting.

Read more about FreshBooks

Users also considered
DealerCenter logo

Dealer management software for independent auto dealerships

DealerCenter is a dealer management system for independent car sales, with mobilized features for inventory tracking, desking, lending and document management

Read more about DealerCenter

Users also considered
Xero logo
Category Leaders

Cloud-based accounting software for small businesses

Xero is an award-winning online accounting software designed for small business owners and accountants, available on any computer or mobile device with an internet connection. Automate your invoicing and reporting, get a full picture of your business with up-to-date financial data, and much more.

Read more about Xero

Users also considered
QuickBooks Desktop logo

Comprehensive business management solution

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.

Read more about QuickBooks Desktop

Users also considered
SAP Concur logo

Travel, expense and invoice, automated and in control

SAP Concur is a leading cloud-based spend management solution that helps small, medium, and large businesses automate and simplify expense reporting, travel booking, and invoice processing. It’s designed to give organizations better control over their business spend by integrating near real-time data and using AI to audit 100% of transactions.

Read more about SAP Concur

Users also considered
Zoho Invoice logo

Online invoicing tool for freelancers and SMBs.

Zoho Invoice is an online invoicing software for freelancers and small to medium enterprises (SMEs). It helps you craft professional invoices, send payment reminders, and get paid faster online.

Read more about Zoho Invoice

Users also considered
NetSuite logo

AI-powered cloud-based business management suite

NetSuite AI-powered accounting simplifies the process of recording transactions, managing AP and AR, and closing the books. NetSuite supports multiple currencies, languages, and compliance standards and ensures data is accessible securely worldwide.

Read more about NetSuite

Users also considered
Abby logo

Billing and invoicing platform

Abby helps businesses ensure that customer documents are legal and comply with the rules. Customers can pay online and receive reminders for late payments.

Read more about Abby

Users also considered
QuickBooks Online Advanced logo

Accounting & business management for small businesses

Advanced accounting software for streamlined financial management, automation, and enhanced reporting for growing businesses.

Read more about QuickBooks Online Advanced

Users also considered
Stampli logo

Stress-free finance operations

Stampli's AP automation solution, made for Accounting teams, centers on the AP process to drive efficiency across the procure-to-pay lifecycle — including payments, credit cards, vendor engagement and more.

Read more about Stampli

Users also considered
BQE CORE Suite logo
Category Leaders

Cloud-based firm management tool for A&E firms.

Accounting Software for Professional Services Firms. BQE Core allows you to watch the books and run your business with ease.

Read more about BQE CORE Suite

Users also considered
BigTime logo

AI-powered scoping, project, time, and billing software

BigTime is a cloud-based platform for professional services firms to manage projects, time tracking, billing, and resource planning—powered by AI. With deep integrations and enterprise-grade security, BigTime helps teams move faster and scale with confidence.

Read more about BigTime

Users also considered
Odoo logo
Category Leaders

All-in-one open-source business software

Odoo Accounting helps you to manage your daily accounting easily and have a global view of the state of your business. Features include: bank synchronization, automatic invoices, recurring billing management, reconciliations, and more.

Read more about Odoo

Users also considered
Patriot Accounting logo
Category Leaders

Cloud-based accounting and payroll software

Accounting Basic $20/month - flat rate, unlimited use
Accounting Premium $30/month - flat rate, unlimited use
Accounting Software for businesses in the United States. Keep track of all of your money easily with our patent pending cash to accrual toggle & so much more.

Read more about Patriot Accounting

Users also considered
KidKare Food Program logo

Childcare platform for home providers and daycare centers

KidKare is a childcare platform that allows home providers, daycare centers, and food sponsors to manage meal programs, claims processing, and accounting operations. Key features include menu management, reporting, customizable templates, regulatory compliance, and access control.

Read more about KidKare Food Program

Users also considered
Cin7 Core logo

Inventory management software for SMBs

Cin7 Core is a cloud-based, inventory and order management application for SMBs which offers a complete back end management solution with purchasing, sales, warehouse management, and light manufacturing features as well as shipping, eCommerce and payment gateway integrations

Read more about Cin7 Core

Users also considered
Cin7 Omni logo

Cloud-based inventory management solution

Cin7 Omni makes complex retail and wholesale simple, with all-in-one Inventory Management, POS, Direct EDI Integration and 3PL integration.

Read more about Cin7 Omni

Users also considered
Premier Construction Software logo

One Modern Platform. 360° Visibility.

All-in-one financial & project management construction cloud ERP, providing you with real-time visibility into your business.

Read more about Premier Construction Software

Users also considered

Key features for Accounting software

Based on GetApp's analysis of verified user reviews collected between July 2021 and August 2024.

  • Income & Balance Sheet: Reviewers value the feature for providing comprehensive financial insights with real-time data, supporting informed decision-making, and offering customizable reports for various business needs. 96% of reviewers rated this feature as important or highly important.
  • Financial Reporting: Users appreciate the ability to generate customizable, real-time financial reports that provide actionable insights and meet diverse business requirements. 94% of reviewers rated this feature as important or highly important.
  • General Ledger: Reviewers highlight the general ledger's comprehensive tracking, real-time updates, and integration with other modules, aiding in accurate financial management and decision-making. 92% of reviewers rated this feature as important or highly important.
  • Billing & Invoicing: Users find the billing and invoicing feature efficient and user-friendly, with automation capabilities that streamline the process and reduce errors. 91% of reviewers rated this feature as important or highly important.
  • Bank Reconciliation: Reviewers commend the feature for simplifying the reconciliation process, ensuring financial accuracy, and saving time through automation and easy integration with bank accounts. 90% of reviewers rated this feature as important or highly important.
  • Expense Tracking: Users appreciate the robust expense tracking capabilities, which facilitate accurate categorization, real-time monitoring, and efficient financial management. 90% of reviewers rated this feature as important or highly important.