9.2
Editor’s Rating:
Best Overall
Cliniko: Appointments
Cliniko
  • Comprehensive practice management solution
  • Streamlined appointment scheduling
  • Comprehensive practice management solution
9.0
Editor’s Rating:
Runner-Up
Lytec: Scheduler
Lytec
  • Specialty-specific billing templates
  • Powerful reporting and analytics
  • Powerful reporting and analytics
8.9
Editor’s Rating:
Also Great
NueMD: Patient File
NueMD
  • Customizable electronic health records
  • Easy-to-use patient portal
  • Customizable electronic health records

HIPAA compliant accounting software provides audit trail capabilities for protected health information (PHI), sets user permissions, and includes a Business Associate Agreement (BAA) from a vendor which guarantees compliance with HIPAA standards. To maintain HIPAA compliance in an accounting system, it needs to adhere to HIPAA rules for handling PHI and withstand a 3rd party audit for adherence to HHS’s OCR audit protocol.

Many software programs can be used in a compliant manner. By definition, any software that avoids HIPAA violations is technically HIPAA compliant. There is no governing body that will officially stamp a software as being HIPAA compliant.

That being said, there are some commonly used accounting software used in medical offices that do a great job at keeping you HIPAA compliant–and we’ve reviewed them for you!

1 Cliniko

Cliniko is a comprehensive practice management solution that offers robust accounting features alongside appointment scheduling and patient management tools. It stands out as an exceptional option for HIPAA complaint accounting due to its comprehensive suite of features tailored to the healthcare industry.

One major strength of Cliniko is strong encryption and data security measures. This ensures compliance and protects sensitive patient information in accordance with HIPAA regulations.

Beyond accounting, Cliniko integrates appointment scheduling and patient management tools–enabling healthcare providers to streamline their admin tasks and focus on delivering quality care.

Users praise Cliniko’s intuitive interface, responsive support team, and seamless integrations with other healthcare software. Along with an intuitive user interface that simplifies the learning curve for staff members, Cliniko is our top choice for healthcare providers seeking a HIPAA compliant accounting software that simplifies practice management and elevates patient care.

Best Overall:
Cliniko

Cliniko: Appointments
Cliniko: Health Records
Cliniko: Transactions
Cliniko: Reporting
Cliniko: Business Management
What We Like
Comprehensive practice management solution
Streamlined appointment scheduling
Comprehensive practice management solution
What We Don’t Like
SMS messages are an additional fee
Only supports basic e-prescription functionality
Overview
Price Range: $$
Starting Price: $45/month
Client OS: Web
Deployment: Cloud Hosted

2 Lytec

Lytec works great for HIPAA compliant accounting while operating fully as a medical billing and practice management software. Catering to a wide range of medical specialties, this options becomes a versatile choice for healthcare providers of all sizes.

The software’s HIPAA compliant features include specialty-specific billing templates, robust encryption, and customizable access controls. This streamlines the billing process by addressing the nuances of various medical disciplines–enhancing efficiency and minimizing errors in your practice’s financial management. It also ensures you can confidently rely on Lytec to product your patient’s data.

Lytec’s user-friendly interface and exceptional support team make it a popular choice among healthcare providers, which is why we recommend it.

Runner Up:
Lytec

Lytec: Scheduler
Lytec: Billing
Lytec: Mobile Patient Intake
Lytec: Patient Demographics
Lytec: ICD-10 Mapping
Lytec: Day Sheet Transaction
What We Like
Specialty-specific billing templates
Powerful reporting and analytics
Powerful reporting and analytics
Overview
Price Range: $$
Starting Price: $69/month
Client OS: Web
Deployment: Cloud Hosted

3 NueMD

NueMD can also operate as a fantastic choice for HIPAA compliant accounting due to it’s cloud-based electronic health records (EHR) and medical billing capabilities that prioritize ease of use and customization.

HIPAA compliance is a core focus of NueMD, which offers strong encryption and strict access controls to protect sensitive data. This ensure sensitive patient data is protected.

A features that stands out for NueMD is its easy-to-use patient portal, which streamlines communication and collaboration between patients and providers.

In addition to being user-friendly, NueMD is one of the most customizable HIPAA compliant accounting solutions on the market. For example, billing reports can be customized, and account info can be accessed on-demand.

Also Great:
NueMD

NueMD: Patient File
NueMD: Check-In Activity
NueMD: Insurance Code Selection
NueMD: Claim Scrubbing
NueMD: Mobile Screen
NueMD: Patient Scheduling
What We Like
Customizable electronic health records
Easy-to-use patient portal
Customizable electronic health records
Overview
Client OS: Web
Deployment: Cloud Hosted

4 Sage Intacct

While Sage Intacct is first and foremost a comprehensive financial management solution with no target industry in mind, the solution boasts robust accounting features and multi-dimensional reporting capabilities which can adhere to HIPAA regulations.

By providing strict data security measures, Sage Intacct ensures the protection of sensitive patient information. Since any software that avoids HIPAA violations is technically HIPAA compliant, Sage Intacct has marketed itself as a top choice for medical practices looking to securely store protected health information (PHI).

The biggest advantage Sage Intacct has over solutions that were built with the healthcare industry in mind is it’s powerful reporting capabilities. This lets healthcare providers get a deeper insight into their financial info by analyzing trends and identifying opportunities for improvement. For example, Sage Intacct can segment revenue by department, location, or physician–providing valuable insights for resource allocation and budgeting.

Sage Intacct’s user experience is bolstered by its intuitive interface, responsive support team, and seamless integration with other systems.

Also Great:
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
Robust financial management features
Multi-dimensional reporting capabilities
Multi-dimensional reporting capabilities
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

Applications found in HIPAA compliant accounting software will provide compliance to ensure you can provide accurate and timely medical billing. This includes end-to-end claim tracking, checks and balances, patient scheduling, insurance billing, and ICD-10 compliance.

HIPAA compliant accounting systems are mostly used by small to mid-sized medical practices, clinics, and allied health professionals. These systems may be marketed as generic accounting systems that are HIPPA compliant, medical practice management solutions, or medical billing software. To decide which one will work best for your organization, you’ll need to decide which additional features beyond core accounting are important to you.

What Is HIPAA Compliant Accounting Software?

HIPAA compliant accounting software provides audit trail capabilities for protected health information (PHI), sets user permissions, and includes a Business Associate Agreement (BAA) from a vendor which guarantees compliance with HIPAA standards. To maintain HIPAA compliance in an accounting system, it needs to adhere to HIPAA rules for handling PHI and withstand a 3rd party audit for adherence to HHS’s OCR audit protocol.

HIPAA compliant accounting software can be a medical accounting software (either on-premise or cloud-based) that was created for the healthcare industry and can handle any liabilities involved in managing protected health information. It can also be a generic accounting solution that has been successfully implemented into medical environments and has vendor-backing that reassures the ability to handle PHI in a compliant manner.

Accounting features found in HIPAA compliant accounting software are typical with those found in standard accounting systems, such as accounts payable (AP) for buying medical supplies, accounts receivable (AR) for medical billing (billing both insurance and patients), and a general ledger to evaluate the company’s income and expenses in real-time.

Cliniko Transactions HIPAA Compliant Accounting Software
Some medical practice management solutions such as Cliniko operate their invoicing and expenses in a HIPAA compliant manner.

Understanding HIPAA Compliance in Accounting Software

The Health Insurance Portability and Accountability Act (HIPAA) is a federal law that regulates the privacy and security of patient health information. This legislation has far-reaching implications for accounting and financial management, requiring organizations to implement stringent data protection measures. Key elements of HIPAA compliance in accounting software include robust encryption, access controls, and audit trails to ensure the confidentiality, integrity, and availability of sensitive data.

Features of HIPAA Compliant Accounting Software

  • Medical Billing: Includes claims management, handle remittances, patient payments, insurance payments, payment processing via credit card or ACH.
  • Audit Trail Management: Monitor when members log in, failed login attempts, software update history, downloads of records, password management, information accessed, what ePHI was changed and by whom, and more.
  • User Permissions: Limit the roles of specific users so that only the correct personnel have access to sensitive medical data. Make sure any data that is received, processed, or transmitted is only accessed by the correct users.
  • Accounts Payable: Invoice processing, payables approvals, and executing payments made by the organization for medical office supplies or other business expenses
  • Accounts Receivable: Manages customer debt collection. Includes customer database management, invoice creation, interest and late fee application, recurring billing support, and more.
  • General Ledger: Reports on the company’s assets, liabilities, revenue, and expenses.
  • Medical Practice Management: Includes scheduling and appointment management and tracking patient communication.
Kareo Billing Insurance Collections HIPAA Compliant Accounting Software
Kareo Billing can manage collections from insurance agencies.

Benefits of HIPAA Compliant Accounting Software

Some of the top benefits of HIPAA compliant accounting software include:

Meet New Regulatory Standards

Health regulations and standards are constantly changing. On top of that, new accounting challenges may appear within your organization that leaves you curious about how you can stay compliant while still providing the financial management your practice deserves.

You’ll want to have a strong relationship with your HIPAA compliant accounting software vendor. Anytime a new software functionality is developed or an update occurs to your accounting system, you know you’ll have a dependable person you can rely on to explain how it affects your compliance concerns.

Medisoft Transaction Entry HIPAA Compliant Accounting Software
Software such as Mckesson Medisoft are developed to meet regulatory standards in recording transactions.

Stay Within The HITECH Act Guidelines

The Health Information Technology for Economic and Clinical Health (HITECH) Act was signed into law back in 2009 after the American Recovery and Reinvestment Act of 2009. In the health industry, the Recovery Act, or ARRA, works as a stimulus package to invest in infrastructure. Its purpose is to promote the use of technology, which led to many health organizations looking to improve their current EHR systems.

The goal of HITECH is to promote meaningful use, which in part established some rules and regulations:

  • It set up four categories of violations
  • It set up four tiers of penalty amounts that increase with each violation
  • It capped the maximum penalty at $1.5M for all violations of an identical provision

In terms of HIPAA compliant accounting software, HITECH sets forth punishment that organizations can face for wilful neglect when it comes to handling sensitive medical information. Many organizations look to make sure they are HIPAA compliant to avoid having to deal with any imposition of penalties as laid out from the HITECH Act.

Sage Intacct Financial Report Editor HIPAA Compliant Accounting Software
Some industry-neutral accounting software such as Sage Intacct have value added resellers that are specialized in implementing in a healthcare setting.

HIPAA Compliant Accounting Software vs. Medical Billing Software

In the medical community, there is much debate as to whether you should pursue a HIPAA compliant accounting software, or go with a medical practice management software that includes medical billing as a primary feature. Some software professionals argue that any confidential patient information relevant to HIPAA should not be stored in accounting software, and even go as far as to suggest using specialized software developed specifically for medical billing.

Without a dedicated accounting system tied into your medical practice management tool, standard accounting workflows may be difficult to accomplish at your organization. Health offices need to bill both insurance agencies and the patient, or even collect co-pays with cash in hand. All of your patient information can be stored in practice management solution, but how do we easily transfer their billing info into the accounting program? This situation can lead to many cases of duplicate entry which can be a loss of time for your organization.

Many software programs can be used in a compliant manner. By definition, any software that avoids HIPAA violations is technically HIPAA compliant. There is no governing body that will officially stamp a software as being HIPAA compliant. Whether the software is marketed as HIPAA compliant accounting software or as medical billing software, you can rest easy knowing they are providing you with the same functionality.

You’ll want to make sure your accounting software provider is a covered entity, which means they are handling your ePHI in a compliant manner. This means any invoice you are sending out to your patients or the insurance companies will not be in any sort of violation.

Is QuickBooks HIPAA Compliant?

While QuickBooks Online does provide adequate online security on par with accounting industry standards, it is not compliant with HIPAA standards for privacy.

Many smaller medical practices may find comfort in the familiarity, ease-of-use, and inexpensive price of QuickBooks. When it comes to patient billing and refunds, it’s natural to want to use your core accounting program of QuickBooks. However, patient names, addresses, and medical record numbers are PHI and should not be used within QuickBooks.

While QBO can do invoicing, it was not designed to handle medical billing. Things like insurance invoices, cash payouts, deductibles, and co-pays are best used by your HIPAA compliant accounting software or medical billing solution.

Can QuickBooks Online Be Used At All In My Medical Office?

If you are creating an invoice for a customer that includes their name, address, and account number with a non-HIPAA compliant cloud-based solution, that can be considered to be violating HIPAA regulations via federal law. There are workarounds that can prevent you from facing HIPAA violations, which include:

  • Using a unique identifier for a patient: Rather than using the medical record number or their account number, you can use a unique customer ID. Your staff will have to do a bit of extra work to match the unique customer ID with their medical record number, but as long as anything considered PHI is not recorded in QuickBooks, you won’t be in violation of HIPAA.
  • Avoid account numbers altogether: If you are printing a refund check or an invoice that will be mailed to your patient, you can simply choose to include their name and address. The issue isn’t even about the information that is on the invoice or refund check. The issue lies in what information is stored digitally in your QuickBooks program itself. As long as no PHI is stored in the program (mainly their medical record numbers) then you won’t be in violation.
  • Summarize your revenue: By using sales summary receipts or invoices to record revenue by service, by the insurance company, or by patient type, as long as you avoid using any PHI you are free to categorize this information into QuickBooks Online.

While you may not be able to look up patient records and check their personal care history in QuickBooks Online, you can still monitor the ongoing financial performance of your clinic on a month-to-month or year-to-year basis. You can break down revenue that is brought in from insurance companies, cash-paying patients, and monitor expenses that were specifically for performing treatments.

The bottom line is while it is possible to use QuickBooks Online in your medical practice, patient health information must be de-identified and protected.

What Does My Medical Practice Need?

No matter what size your healthcare organization may be, you’ll want to make sure you have the right set of functionalities to meet your most pressing needs.

  • Small medical practices will want to be able to handle their medical billing, have notifications for patients that are late on payments, track which suppliers require payment, and monitor the contact attempts to collect on these debts (or pay on your own debts). Usually, a system with only one-user license is sufficient if you will only have one accountant or bookkeeper accessing the software.
  • Mid-sized medical practices will want to look into software that lets you set user permissions. These practices likely have more users needing access to the software, so you will want to limit what type of access they have and the information they can readily view. With increased users in the system, you’ll also want a quality audit trail that records log-in times, changes made to files, who made these changes, etc. In the case of any information breach, you should be able to track down any involved individuals.
  • Large medical practices may need to integrate with electronic health record systems (EHR software) or look into fully integrated hospital management software to ensure they have all of their functionality under one solution. This can limit the exchange of information between programs and ensure all of your data is secure within one system.

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
Cliniko Screenshot
Cliniko is a complete medical practice management solution for clinics and allied health practioners. Key features include appointment scheduling, treatment notes, online booking, electronic health records (EHR), and invoicing, among others. It streamlines administrative tasks significantly for healthcare providers and ensures high security for patient data. The software also offers telehealth functionality, making it suitable for telemedicine practices​. Cliniko software is accessible via mobile web browsers. It integrates with Xero for accounting and Mailchimp for email marketing.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$45/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
Better Clinics Screenshot

Better Clinics

Better Clinics is a clinic management software providing appointment scheduling, online booking, customer management, invoices, marketing, and team management. Better Clinics is an online solution intended for use by health and fitness professionals. Note : This product is only available in Australia, New Zealand, and the UK. Better Clinics provides features to manage your entire clinic: Anywhere access; Patient appointment scheduling; Wait lists; Personalization; Reduce no-show rates; and Syncs
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$13.31/month
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
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
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
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
SAP Business One Screenshot

SAP Business One

★★★★★
★★★★★
(11)
SAP Business One provides comprehensive business management capabilities for small and medium-sized companies. This system provides integrated departmental support for finance, sales, supply chain management, production, project management, and production processes. This software can be deployed on-premise or on the cloud, and accessed from any mobile device through iOS and Android apps. The SAP API Business Hub allows for a wide range of partner integrations.
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$410/user/year
Client OS
Windows
Deployment
Cloud or On-Premises
CGM Medisoft Screenshot

CGM Medisoft

Designed to support small, independent physicians, CGM Medisoft is a proven practice management system that delivers streamlined scheduling and billing functionality along with complete revenue management capabilities. CGM Medisoft’s newly-released mobile computing technology and support for ICD-10 codes gives your practice the tools needed to improve efficiencies and manage increasing regulatory compliance requirements. @youtube With the latest CGM Medisoft release, the solution becomes CGM
Price Range
   $     $     $     $     $   
   $     $     $     $     $   
Starting Price
$69/user/month
Client OS
Web
Deployment
Cloud Hosted
AdvancedPM Screenshot

AdvancedPM

★★★★★
★★★★★
(4)
AdvancedPM from AdvancedMD is a complete practice management and medical billing software for private practices and billing services. The solution provides front office functionality, billing software, and reporting capabilities. AdvancedMD PM also lets you simplify your A/R tracking with a claims management feature and scheduling integration. Features of AdvancedMD PM include: Insurance eligibility verification; Appointment reminders; Schedule snapshot; Quick-look summaries; Quick-add
Client OS
Windows
Deployment
On-Premises
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

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.

Sort by 
Filter by User Rating
Filter by Price Range
Filter by Deployment
Filter by Client OS
Talk with a software advisor
Talk with an advisor
Get a free consultation from an independent software expert.
Or, call toll-free: (800) 827-1151
Talk with a software advisor
Talk with an advisor