Best Accounting Software for Healthcare Organizations

Table of Contents

1. Why Healthcare Needs Specialized Accounting Software
2. Top Accounting Software for Healthcare Organizations
3. How Paystand Helps Healthcare Organizations Automate Receivables

Key Takeaways

• Leading cloud-based accounting platforms like NetSuite, Sage Intacct, and Acumatica offer healthcare-specific financial tools.
• Healthcare organizations benefit from automation that improves cash flow, ensures compliance, and reduces manual processes.
• Paystand helps accelerate B2B healthcare payments and modernize receivables.

Why Healthcare Needs Specialized Accounting Software

The financial systems used by healthcare organizations must do more than generate financial statements. They must safeguard protected health information, ensure compliance, and deliver secure audit trails, enabling finance teams to eliminate manual tasks and optimize cash flow.

Manual processes are costly and outdated in a space where reimbursements often lag 30 days or more. This is why modern cloud accounting software is essential. By streamlining expense tracking, accounts payable, and real-time reporting, healthcare teams can make smarter decisions, faster.

Want to learn more about the rise of digital payments in healthcare and why paper checks are becoming obsolete? Read our latest analysis.

Top Accounting Software for Healthcare Organizations

NetSuite

NetSuite is a market leader in cloud-based ERP systems for healthcare organizations with complex operations or multiple locations. It’s trusted for its robust financial modules and seamless integration capabilities.

Why It Stands Out:

• Centralized financial controls with multi-entity support
• Configurable workflows for medical practice billing
• NetSuite Marketplace integrations for healthcare-specific apps

Sage Intacct

Sage Intacct is built to serve industries like healthcare where compliance and security are mission-critical. Its ability to automate financial processes and maintain HIPAA standards makes it a favorite among CFOs in the sector.

Why It Stands Out:

• Healthcare-specific reporting
• Transparent audit trails for regulatory compliance
• Optimized for handling 30-day payment cycles and donor/grant tracking

Acumatica

Built for flexibility, Acumatica is ideal for mid-sized healthcare providers that want to digitize their financial operations without sacrificing customization.

Why It Stands Out:

• API-friendly for integrations with EHR and CRM
• Scalable for growing provider networks
• Supports full automation of accounts payable and real-time visibility

Microsoft Dynamics 365

Dynamics 365 brings together financials, patient engagement, and operations on a single platform. It’s particularly strong for hospital networks already using the Microsoft ecosystem.

Why It Stands Out:

• Rich automation and AI features
• Deep reporting across all aspects of healthcare accounting
• Integration with Microsoft Teams and Power BI

QuickBooks

A practical choice for independent practices and health consultancies, QuickBooks offers user-friendly tools for everyday accounting, including credit card processing and invoice generation.

Why It Stands Out:

• Simplified expense tracking
• Affordable for smaller healthcare offices
• Fast setup and onboarding

Xero

Xero is a great fit for small medical practices seeking accessible cloud accounting software that handles daily transactions and financial reporting.

Why It Stands Out:

• User-friendly dashboard and mobile app
• Clean interface for reconciliations and invoicing
• Cost-effective for small teams

How Paystand Helps Healthcare Organizations Automate Receivables

Once you have the right accounting system in place, the next step is accelerating how you get paid. That’s where Paystand’s healthcare solution comes in.

In an industry with narrow margins and delayed reimbursements, Paystand transforms the way healthcare organizations collect revenue:

• Automate invoice reminders, follow-ups, and payment options
• Reduce days outstanding—get paid faster than 30 days
• Accept digital payments while avoiding credit card fees
• Provide a seamless experience for payers, patients, or partners
• Connect directly to NetSuite, Acumatica, Sage Intacct, and other platforms
• Gain real-time insight into your cash position

Curious how this fits into the broader B2B ecosystem? Explore our breakdown on B2B healthcare payments and why the shift to cashless healthcare is accelerating.

Looking for deeper insights? Don’t miss our post on healthcare payments modernization and what’s changing in 2025.

Get Started With Paystand

In the healthcare industry, every dollar and every day counts. With Paystand, you can cut out paper checks, automate your receivables, and ensure your financial system is as modern and secure as your practice.

Learn more about how Paystand enables healthcare finance teams to improve operations, boost cash flow, and drive better patient outcomes.

Explore Paystand for Healthcare.