8.7
Editor’s Rating:
Best Overall
Sage Intacct: Purchasing
Sage Intacct
  • Multi-dimensional reporting capabilities
  • Scalability for multi-entity support and user growth
  • Simple and responsive user interface
8.3
Editor’s Rating:
Best for Hospitals and Large Medical Practices
NetSuite ERP: Home Screen
NetSuite ERP
  • Hundreds of third-party add-ons available
  • Feature sets for multiple industries
  • Highly customizable
8.5
Editor’s Rating:
Best for Private Practices
FreshBooks: Dashboard
FreshBooks
  • Customizable payment terms
  • Discounted intro pricing
  • No setup costs

Medical accounting software manages and tracks financial operations within healthcare facilities, streamlining billing, payroll, and budgeting processes. We used our review methodology to review and rank our favorites.

1 Sage Intacct - Best Overall

Why We Chose It: We chose Sage Intacct as our top pick due to its industry-specific features for growing healthcare facilities. Unlike many other accounting software options, Intacct includes security, access controls, and audit trails that comply with HIPAA standards. This way, healthcare professionals can manage their reports and financial data while ensuring they follow the requirements around PHI. This software also includes financial statements and healthcare-specific reports that obey IRS standards.

We gave Intacct a score of 8.7 for its simple interface and real-time, multi-dimensional reporting capabilities. This software can integrate data from payroll, electronic medical records, and CRMs like Salesforce. However, Sage doesn’t include pricing on their website, though it’s comparable to costs for other enterprise-level general ledger software like NetSuite.

Best Overall:
Sage Intacct

Sage Intacct: Purchasing
Sage Intacct: Entities
Sage Intacct: Order Entry
Sage Intacct: Resource Search
Sage Intacct: Report Center
Sage Intacct: Financial Report Editor
Sage Intacct: Dashboard
What We Like
Multi-dimensional reporting capabilities
Scalability for multi-entity support and user growth
Simple and responsive user interface
What We Don’t Like
Budgeting and interactive reporting cost extra
Limited non-financial functionalities
Volume exports can be difficult
Overview
Price Range: $$$
Starting Price: $8,580/year
Client OS: Web
Deployment: Cloud Hosted

2 NetSuite - Best for Hospitals and Large Medical Practices

Why We Chose It: Although NetSuite isn’t marketed as healthcare accounting software, there are many reasons why we found it suitable for large medical practices and hospitals. We gave the platform a score of 8.3 for its financial management and accounting tools integrated with other functions like billing, compliance management, and inventory. This streamlines clinical, financial, and operational processes for healthcare professionals on a single platform.

NetSuite also complies with accounting standards like GAAP and can help companies meet their requirements with audit trails and real-time compliance monitoring. It can also benefit a company with other international locations by offering global account management, multi-currency support, and language interfaces. However, our research shows many reviewers found the software expensive and required multiple add-ons, which increased the overall price.

Best for Hospitals and Large Medical Practices:
NetSuite ERP

NetSuite ERP: Home Screen
NetSuite ERP: Income Statement
NetSuite ERP: Journal
NetSuite ERP: Unrealized Exchange Rate Gains and Losses
NetSuite ERP: Ecommerce Customer Statistics
NetSuite ERP: Sales Orders
NetSuite ERP: Revenue Recognition
What We Like
Hundreds of third-party add-ons available
Feature sets for multiple industries
Highly customizable
What We Don’t Like
Must schedule a consult for pricing details
Tedious setup
Difficult to build reports
Overview
Price Range: $$$$
Starting Price: $99/user/month
Client OS: Web
Deployment: Cloud Hosted

3 FreshBooks - Best for Private Practices

Why We Chose It: After using a free trial and testing FreshBooks for ourselves, we found this software a top choice for private practices or independent clinics. We gave FreshBooks a score of 8.5 because it can manage various bookkeeping needs, such as time and expense tracking, invoicing, and cash-flow management. With these features, we recommend this software for mental health practices and consultation-based specialties, especially if they charge by the hour or session.

We also like that FreshBooks features seamless integration options that allow practices to manage payroll and appointment scheduling through the accounting software. Some standard services and apps FreshBooks integrates with include PayPal, Gusto, Salesforce, and Microsoft Office 365. FreshBooks allows practices to create customizable invoices with their branding and logos. Businesses can then send recurring invoices to ongoing patients, accept online payments, and have recurring billing through templates.

However, FreshBooks may not be the software for you if you have more than one or two people on your accounting team as it limits the number of users in all plans. This software also doesn’t offer HIPAA compliance.

Best for Private Practices:
FreshBooks

FreshBooks: Dashboard
FreshBooks: Add Ons
FreshBooks: Mobile Dashboard
FreshBooks: Accounting Settings and Reports
FreshBooks: Advanced Accounting
FreshBooks: Bank Connections
FreshBooks: Mileage Tracking on Mobile
FreshBooks: Email Templates
FreshBooks: Expense Report
FreshBooks: Invoice From Unbilled Hours
FreshBooks: Mobile Trip Tracking
FreshBooks: Mobile Dashboard
FreshBooks: Mobile New Invoice
FreshBooks: Available Integrations
FreshBooks: Mobile New Invoice
FreshBooks: Add New Client
FreshBooks: Add New Expense
FreshBooks: Payroll Settings
FreshBooks: Create New Invoice
FreshBooks: Time Tracking
FreshBooks: New Project
FreshBooks: View Invoice
FreshBooks: FreshBooks Reports
What We Like
Customizable payment terms
Discounted intro pricing
No setup costs
What We Don’t Like
Client-based pricing
No bulk invoice creation
Limited report customization
Overview
Price Range: $
Starting Price: $19/month
Client OS: iOS, Android, Web
Deployment: Cloud Hosted

4 QuickBooks Desktop Enterprise

Why We Chose It: Due to its scalability, integration, and strong accounting capabilities, QuickBooks Desktop Enterprise is a good choice for small—to medium-sized healthcare organizations with ten to 50 employees. We especially like that it features customizable reporting capabilities to personalize accounts for medical expenses, insurance payors, and procedures.

We also like that QuickBooks offers tools like accounts payable/receivable, invoicing, and inventory management. This software supports up to 40 users simultaneously and can track multiple locations, which can be especially beneficial if a business has multiple providers or facilities.

One drawback of QuickBooks is that it is not HIPAA-compliant; therefore, organizations can’t create or store any protected health information unless the software is used via a third-party hosting service that supports HIPAA compliance. Another downfall is that once a company expands, QuickBooks Desktop begins to show its limitations by restricting the number of users, chart of accounts, and locations.


QuickBooks Desktop Enterprise: Inventory Dashboard
QuickBooks Desktop Enterprise: Company Snapshot
QuickBooks Desktop Enterprise: Payroll
QuickBooks Desktop Enterprise: Income Tracker
QuickBooks Desktop Enterprise: Credit Card Entry
QuickBooks Desktop Enterprise: Company Preference Pane
QuickBooks Desktop Enterprise: Batch Invoices
What We Like
More advanced inventory features than other QuickBooks versions
Higher record capacity than other QuickBooks versions
Includes payroll and employee management
What We Don’t Like
Most expensive version of QuickBooks
Requires annual contracts
Windows only
Overview
Price Range: $$$
Starting Price: $199/month
Client OS: Windows
Deployment: Cloud or On-Premises

5 Zoho Books

Why We Chose It: After testing Zoho Books’ features, we found it suitable for smaller medical practices or solo practitioners with basic accounting needs. It provides capabilities like invoicing, financial reporting, and expense tracking. This software meets the basic bookkeeping requirements at a very affordable price, with free plans for start-up practices or solo practitioners and paid plans starting at only $15 per month.

For small practices without an accounting team, Zoho Books is a great option. It’s very user-friendly, and its mobile app makes it easy to manage an account on the go. Zoho Books also features integration options that could potentially link to medical billing software.

While Zoho Books could be a good option for small practices and start-ups, it lacks specialized features like medical billing or compliance with healthcare regulations like HIPAA.


Zoho Books: Invoicing
Zoho Books: Recurring Bills
Zoho Books: Inventory
Zoho Books: Bank Reconciliation
Zoho Books: Time Tracking
Zoho Books: Contacts
Zoho Books: Dashboards
What We Like
Client portal with sales and purchase approvals
Easily integrate with dozens of Zoho products
Time-tracking
What We Don’t Like
Difficult to modify invoices
Time tracking must be tied to projects
Maximum of 10 users
Overview
Price Range: $
Starting Price: $15/month
Client OS: Web
Deployment: Cloud Hosted

What is Medical Accounting Software?

Medical accounting software helps healthcare providers manage their financial operations, and accounting needs specific to their industry. This specialized accounting software is designed specifically for healthcare providers, medical practices, hospitals, and other healthcare-related organizations.

The best medical accounting software will feature a variety of traditional and medical-based features including streamlined medical billing processing, support for multi-location accounting, and compliance with healthcare regulations.

Sage Intacct Revenue Dashboard
View revenue by industry, territory, and item in Sage Intacct.

Key Features

  • General Ledger (GL): Records all financial transactions like assets, capital, revenue, expenses, and liabilities.
  • Accounts Receivable (AR): Manages all debt (asset) collection from patients, insurance, and vendors.
  • Accounts Payable (AP): Manages all money owed (liabilities) by your hospital to creditors.
  • Payroll: Distributes employee paychecks through direct deposit or check printing. Automates wage calculation based on pay rates and correctly tracks employee tax withholdings.
  • Medical Billing: Generates invoices for distribution to patients and insurance companies. Also organizes billing for organizations like Medicare and Medicaid.
  • Inventory Management: Tracks all assets like medical consumables, office supplies, and cafeteria food.
  • Bank Reconciliation: Matches bank records with your hospital’s general ledger accounts.
NetSuite Revenue Recognition Dashboard
Access the revenue recognition dashboard in NetSuite.

Benefits

Here are the best benefits of hospital accounting software:

Streamlined Communication with Insurance Companies

Healthcare organizations regularly deal with insurance companies when collecting payment for services. Medical billing software generates the claim based on the medical codes provided by your hospital. It is up to your staff to start the billing cycle by updating patient files with the correct procedure codes. Once you have a claim, it can be sent directly to the patient or their insurer. Then you just have to wait for payment.

Unfortunately, insurance companies are notorious for dragging their feet when paying out a claim. And that’s only if the insurance company accepts the claim in the first place without denying coverage. Delayed payments can add up in your accounts receivable and make it hard for you to accurately update your hospital budget. Revenue Cycle Management (RCM) applications streamline the claims process by automating payment processing. When those payments finally do come in, you can rest easy knowing your general ledger is up-to-date.

Track Nonprofit Accounts and Charitable Donations

Many nonprofit hospitals depend on donations to operate at the highest possible standard of care. It’s up to you to keep track of how the money is used by your institution. Hospital accounting software makes it easy to record incoming donations to generate receipts for current donors.

For-profit and nonprofit healthcare institutions usually host fundraisers to raise money for specific departments or causes within the hospital. With accurate donation records, your hospital will know when to plan future fundraising efforts.

Easy Accounting Access from Mobile Devices

Cloud-based accounting software lets you double-check your financial data from smartphones and tablets. You could be in the middle of a boardroom meeting and pull up accurate, real-time information from the general ledger.

FreshBooks Custom Invoicing
Customize invoices in FreshBooks.

How Much Does Medical Software Cost?

The typical starting cost for a single user on a basic plan is between $15 and $100 monthly for the service, not including setup or other fees. However, the price depends on several factors, such as the number of providers and users, the practice size, the features and functionality, and the integration needs with other medical software. Depending on which software best suits your practice, prices could quickly increase to the thousands.

What Software Does My Hospital Need?

The type of software your hospital requires will depend on several factors like size, funding, frequency of inpatient vs. outpatient services, and whether you are a for-profit or nonprofit organization.

  • General hospitals offer any healthcare institution’s widest range of services. As such, their accounting software needs to be just as comprehensive. Your hospital has to be able to accurately bill all your services, like emergency room visits, labor & delivery, and medical imaging. It also needs inventory management of consumables like gowns, gloves, and other single-use materials. You’ll want an ERP-style software suite which offers as many applications as possible.
  • Specialty hospitals always have a specialized function, like serving as a trauma center or only serving pediatric patients. Get specialized accounting software to cover your medical billing. In particular, medical billing and invoicing modules help specialty hospitals stay on top of invoices to patients and insurance companies.
  • Teaching hospitals are a great way for medical students to learn about how the healthcare industry operates. If your teaching hospital is affiliated with a university, your funds may be distributed by the school.
  • Government hospitals, as tax-funded entities, need to be totally transparent with their finances. Use a detailed general ledger application to record all accounts for accurate reporting when it’s time to review your annual budget.

HIPAA Compliant Software for Hospitals

Hospitals have to work with a lot of third-party medical businesses. When handling any sensitive patient information, it’s up to your hospital to protect their privacy and electronic health records (EHR), per the Health Insurance Portability and Accountability Act (HIPAA). HIPAA compliant accounting software allows for the safe transfer of medical billing documents, even if they contain electronic protected health information (ePHI).

Regular accounting software solutions that are not designed for healthcare may not meet HIPAA compliance. To prevent fraud and patient privacy violations, you cannot expose patient records to any person or organization not qualified. Medical billing software is designed to transfer electronic medical records (EMR), EHR, and ePHI in a compliant manner by using secure codes.

QuickBooks Desktop Enterprise Company Snapshot
View income and expense trends, outstanding bills, and account balances in QuickBooks Desktop Enterprise.

Painful Accounting Mistakes

Small mistakes with your accounting can lead to expensive problems for your hospital management. Avoid these common errors:

Missed Medical Billing Mistakes

Medical billing errors are common at hospitals simply because of the daily patient volume. All it takes is one number being entered wrong on a patient chart to lead to an incorrect bill. Patients and insurance companies may fight charges that are incorrect. Make sure all your claims are as accurate as possible to prevent payment delays.

Another issue comes from upcoding, when the medical code entered on a claim does not match the treatment given. In particular, it usually results in a significantly higher bill. Insurance companies will use any evidence of upcoding to try to dismiss an entire claim, so use the right medical billing solution to avoid these costly mistakes.

Denied or Rejected Claims Not Being Collected

Once an insurance company denies or rejects a claim, it’s back on your hospital to handle collections. You need to carefully manage patient communications to ensure you don’t lose money for services rendered.

Denied claims may be appealed, but only if there is a reason for reconsideration. For example, if a procedure isn’t covered by the insurance company in the first place, the claim will always be denied. However, if it turns out the procedure is covered but the wrong code was used, that may have resulted in an accidental denial.

Rejected claims contain some sort of error, such as the aforementioned upcoding or a simple clerical mistake. When an insurance company rejects a claim, your hospital will have to act fast to resubmit a corrected claim.

Zoho Books Recurring Bills
Set up recurring bills in Zoho Books.

All Products

No products found
Sage Intacct Screenshot

Sage Intacct

★★★★★
★★★★★
(46)
Sage Intacct is a browser-based, GAAP-compliant financial management software system. It features multi-entity financial reporting, customizable reports, and a user-friendly interface. The AICPA has endorsed the platform as a “preferred provider of financial management application.”
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$8,580/year
Client OS
Web
Deployment
Cloud Hosted
NetSuite ERP Screenshot

NetSuite ERP

★★★★★
★★★★★
(25)
Oracle’s NetSuite is well-known in the ERP world for its customization and scalability. It’s a multi-tenant ERP software supporting finance, operations, sales, service, and HR needs.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$99/user/month
Client OS
Web
Deployment
Cloud Hosted
FreshBooks Screenshot

FreshBooks

★★★★★
★★★★★
(5)
FreshBooks is well-recognized in the accounting world and stands as a competitor to QuickBooks Online. It’s a simple cloud accounting software that allows you to invoice clients, track expenses, and accept payments.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$19/month
Client OS
iOS, Android, Web
Deployment
Cloud Hosted
QuickBooks Desktop Enterprise Screenshot

QuickBooks Desktop Enterprise

★★★★★
★★★★★
(40)
QuickBooks Desktop Enterprise is a Windows-based accounting system for small to medium businesses. It’s perhaps Intuit’s most advanced platform under the QuickBooks brand, offering more capacity and advanced inventory features. The software’s strong inventory management tools, including advanced tracking and automation, particularly benefit businesses managing complex inventory across multiple locations. [QuickBooks Desktop Enterprise offers cloud access](https://quickbooks.intuit.com/desktop/enterprise/hosting/) as an annual subscription, in addition to its on-premises offering. It also has industry-focused editions with tools and reporting tailored to specific business needs, enhancing customization.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$199/month
Client OS
Windows
Deployment
Cloud or On-Premises
Zoho Books Screenshot

Zoho Books

★★★★★
★★★★★
(6)
Zoho Books is a popular alternative to QuickBooks Online. It’s a cloud-based accounting software that offers accounts receivables and payables functionality. It lets you manage your financials and banking, create reports, and automate your sales and purchasing workflows.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$15/month
Client OS
Web
Deployment
Cloud Hosted
Affinity ERP Screenshot

Affinity ERP

★★★★★
★★★★★
(2)
Harris Healthcare maximizes cash flow for small and medium sized hospitals, healthcare systems and large physician and long-term care organizations with comprehensive ERP, Decision Support, Patient Self-Service, and Revenue Cycle Management software and services. Start maximizing your cash flow with a low price guarantee for fully-integrated or stand-alone software solutions. Finance; Supply Chain Management; Human Capital; Systems Management; Cost Accounting; Contract Management; Budgeting;
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$1,800/year
Client OS
Windows, Web
Deployment
Cloud or On-Premises
athenaCollector Screenshot

athenaCollector

★★★★★
★★★★★
(5)
Conventional medical billing systems give you just software. athenaCollector delivers more, combining cloud-based software, networked intelligence, an efficient workflow and back-office services. Experts take on your most time-consuming tasks, like claim submission and follow-up, denial management, payment posting and more, getting practices paid 6% more, and 32% faster.1 By working at massive scale for over 67,000+ clients, athenahealth drives results with unparalleled accuracy and efficiency.
Deployment
Cloud Hosted
PDS MDsuite Screenshot

PDS MDsuite

★★★★★
★★★★★
(1)
PDS MDsuite by PDSMED outperforms competing systems. First and foremost, it’s easier to use. Its streamlined, time-saving components and integrated features help ensure that you capture all the charges insurance companies will reimburse. Your MDsute practice and records management systems fit you and your operation like a latex glove. Have access to a full patient history — every time. Move the patient from check-in, through the exam to checkout without ever handling a paper chart. Edit and add
Starting Price
$49/month
Client OS
Windows, Web
Deployment
Cloud Hosted
CollaborateMD Screenshot

CollaborateMD

★★★★★
★★★★★
(5)
CollaborateMD is a cloud-based medical billing software that helpsclaims get to the medical insurance payer as quick as possible. The software provides various features like claim control and task management, appointment scheduling, patient processing and payment, and report financials and dashboards. These functionalities aim to improve the efficiency of front office operations and enhance the financial performance of medical practices. The solution works best for small to medium sized practices due to the affordable price and ease-of-use.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$215/month
Client OS
Web
Deployment
Cloud Hosted
Lytec Screenshot

Lytec

★★★★★
★★★★★
(2)
Lytec 2019 is a medical practice management solution providing medical billing and office workflow optimization. Lytec Practice Management is ANSI 5010 compliant, and can manage the scheduling, billing, and revenue management of your practice. Lytec 2019 can be provided as a stand-alone network version or a cloud-based solution. @youtube Accounting —Move credits and adjustments between billings; Engagement —Patient Email Connect allows for a targeted export of 27 different filters such as age,
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$69/month
Client OS
Web
Deployment
Cloud Hosted
NueMD Screenshot

NueMD

★★★★★
★★★★★
(4)
Welcome to NueMD, your complete Internet-based medical billing software solution. The easy-to-use, affordable online medical billing software will help you better serve your clients by shortening their reimbursement cycles, increasing efficiencies within their practices, and providing them with detailed reports on revenue trends, collection aging, and payment status. Because NueMD is Internet-based, it is faster and more secure than Web-based medical billing software. All of your clients can
Client OS
Web
Deployment
Cloud Hosted
Tebra Screenshot

Tebra

★★★★★
★★★★★
(6)
Tebra, formed from the merger of Kareo Billing and PatientPop, is a practice management and healthcare technology platform. It offers a complete operating system for medical practices, encompassing online scheduling, reputation management, telehealth, and in-person appointment reminders. Its real-time analytics provide deep insights for healthcare providers to improve patient well-being and practice growth. The integration of electronic health records (EHR), compliance tracking, and task automation make it a powerful tool for healthcare providers.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Client OS
Web
Deployment
Cloud Hosted
Sage X3 Screenshot

Sage X3

★★★★★
★★★★★
(3)
Sage X3 is an ERP software tailored to automate ecommerce business processes for mid-sized companies. It focuses on enhancing efficiency in process and discrete manufacturing industries by streamlining supply chain management and various business operations. The software stands out with its user-friendly interface, accessibility via web and mobile platforms, and compatibility with Windows OS. It is notable for managing purchase orders effectively and providing insights into business process effectiveness.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$4,500/user (perpetual license)
Client OS
Windows, Web
Deployment
Cloud or On-Premises
ManageMed Screenshot

ManageMed

Medical organizations are often faced with the daunting task of managing numerous receivables. With ManageMed, specifically designed for both insurance and self-pay accounts, collecting those receivables is a much more efficient process. Upon purchasing Columbia Ultimate’s ManageMed, you will enable yourself to manage and set up your own collection strategies. ManageMed is a powerful collection tool specifically designed for reconciling medical receivables. With this automation tool you will be
Client OS
Windows, macOS
Xledger Screenshot

Xledger

★★★★★
★★★★★
(3)
Xledger is a finance, project and Business Information system that gives customers tighter control of their business. This ERP software provides basic accounting, OCR data entry, and mobile access to your company finances. The fully integrated system includes role-based access to control which users can see and interact with each feature.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Client OS
iOS, Android, Web
Deployment
Cloud Hosted

We searched and searched, but we couldn’t find any products in our database that match your criteria. Perhaps our team of software experts can help? They’d be happy to provide a list of free recommendations that meet your exact requirements.

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