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Top Rated Medical Accounting Software with Payment Processing

Last updated: May 2026

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25 software options

Sage Intacct logo

Sage Intacct

Best-in-class Cloud ERP for Finance

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HIPAA-compliant healthcare accounting with departmental costing, revenue cycle, multi-location consolidation, EHR integrations, audit trail.

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Accounting Seed logo

Accounting Seed

Accounting and analytics software built on Salesforce

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Accounting Seed is an accounting application built natively on Salesforce. Its customizable, enabling users to manage their accounting their way. As a full accounting solution, Accounting Seed tracks financial data through the entire business lifecycle.

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QuickBooks Enterprise logo

Enterprise accounting, FSM and inventory management solution

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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.

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Striven logo

Collaborative ERP for business process management

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Striven is a comprehensive business management software suite. It provides a range of features to support organizations across various industries, such as construction, manufacturing, professional services, and field services. The software offers real-time access to critical business data, helping to eliminate issues with missing, lost, or inaccurate information.

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Daxko Operations logo

Membership management software for non-profit organizations

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Complete operations software for member-based nonprofits - integrating programs, billing, and check-ins in one secure system.

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TopNotepad logo

All-in-one software for managing small businesses

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TopNotepad is a cloud-based business management solution for freelancers and small businesses, offering invoicing, accounting and indirect tax (Sales Tax/VAT/GST) compliance solution.

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QuickBooks Online Advanced logo

Accounting & business management for small businesses

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QuickBooks Online Advanced is a web-based accounting & business management solution which enables small businesses to track sales, inventory, financial accounts & payroll from a single dashboard

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ZipBooks logo

Accounting and online invoicing software

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ZipBooks is a cloud-based accounting software that caters to the bookkeeping and accounting needs of small to medium-sized businesses and bookkeeping firms. The solution offers core accounting, financial reporting, online invoicing, expense tracking, credit card processing, and more.

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NextProcess logo

Accounts Payable software for automated invoice processing

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NextProcess accounts payable (AP) software integrates with existing ERPs to accurately automate invoice processing, route approvals and add vendor self-services

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GipoNext logo

The all-in-one software solution for clinics

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GipoNext is a 100% cloud-native clinic management software to digitize the whole patient journey.

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SapphireOne logo

Enterprise Resource Planning software

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SapphireOne streamlines medical accounting with tailored features for healthcare, ensuring accurate billing, invoicing, and compliance. Real-time data integration enhances efficiency in managing patient accounts and claims. Customisable reports offer insights, while scalability supports growth.

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FINSYNC logo

Powerful Partnerships Simplified Finances Stronger Business

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FINSYNC helps entrepreneurs and small business owners simplify operations and secure affordable funding through one connected platform.

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AcuSheet logo

Simple Accounting Software

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AcuSheet is easy to use accounting and invoicing software to track and manage your finances so you can focus more on your business.

AcuSheet helps businesses manage accounts in the background to ensure compliance and also generates financial reports.

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Rerun logo

Recurring billing. Simplified.

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Rerun is for any small business, organization or association that wants to automate their recurring, subscription or membership billing.

Rerun integrates with AccountEdge, QuickBooks and Xero to help your business run efficiently.

Get started for FREE.
Pay only for what you process.
2.9% + $0.30 per transaction.

Free 30-day trial.
No credit card required.

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Billed logo

Invoicing & accounting software for small businesses

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Billed is an invoicing and accounting software designed for small businesses to get paid faster. It offers features such as online invoicing, expense tracking, time tracking, recurring invoices, and credit card payments to streamline financial management. Billed also provides project management tools, financial reporting, and the ability to manage multiple businesses from a single platform, empowering small business owners to focus on growth.

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Sage 50cloud Pastel logo

Effortless accounting for growing businesses.

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Sage 50cloud Pastel Partner is a powerful desktop accounting solution connected to the cloud, offering in-depth stock and reporting features. It provides smart cloud-connected accounting software with productivity-boosting features like direct bank feeds, cloud document storage, and integrated payments. Sage 50cloud Pastel Partner helps growing businesses run their operations more efficiently with its time-saving solutions for managing accounting, invoicing, cash flow, inventory, and VAT.

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InvoiceSherpa logo

Invoice payment reminder app

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InvoiceSherpa is an invoice management and debt recovery application that helps to track and follow up with overdue payments. It integrates with major accounting apps, automatically extracting invoice and customer data from the core accounting software, and updating the data when payments are made.

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CenterPoint Accounting logo

Accounting Software for Growing Businesses

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Accounting Software for growing businesses. CenterPoint Accounting Software works especially well for those outgrowing basic accounting systems, those requiring flexible financial reporting, and the management of multiple companies.

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Zoho Books logo

Online accounting software for businesses of all sizes

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Zoho Books is an online accounting software designed to streamline back office operations, automate workflows, and allow secure collaboration with accountants

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QuickBooks Online logo

Accounting and business management software

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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.

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NetSuite logo

AI-powered cloud-based business management suite

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NetSuite is an AI-powered cloud-based business management suite. It helps organizations streamline their operations and gain real-time insights into their performance. The suite caters to a range of industries such as manufacturing, retail, and professional services.

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SAP Concur logo

Travel, expense and invoice, automated and in control

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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.

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Melio logo

Accounts payable platform for businesses of all sizes

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Melio offers a B2B payments solution for businesses of all sizes, letting you pay vendors by bank transfer or card—even in cases where cards aren't accepted. Effortlessly sync with QuickBooks and Xero, automate payment scheduling, and create custom approval workflows.

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Sage 100 logo

Enterprise resource planning software

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Sage 100 is a customizable business management solution that helps businesses automate financials, operations, and payroll, providing complete visibility into the operations. Sage 100 grows with the business, allowing teams to scale and meet specific needs as a small or medium-sized enterprise.

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Sage Accounting logo

Accounting software for small businesses

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Sage Accounting is an accounting system for small business owners. It has features to help users forecast their cashflow, send and track invoices and act on real-time reporting. Users can manage their business from anywhere, at any time, from the cloud and with mobile functionality. Sage Accounting application is available for iOS and Android.

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