HIPAA eCommerce

HIPAA-Compliant Billing Software: Protecting ePHI During Invoicing

Updated April 29  |  5 min read

Whether your business sells physical products like prescriptions or offers healthcare services, invoices will probably play a part. While some people may pay immediately, the inclusion of insurance and bulk purchasing (as occurs in B2B eCommerce) means that invoicing will be something you need to plan for. This includes a plan for how you want your business to grow in the years to come.

HIPAA-compliant accounting software as a practice management solution.

HIPAA-covered information must have two seemingly opposite properties. It needs to be incredibly secure, but at the same time it needs to be easily accessible with short notice. These needs can both be met with proper planning. When it’s time to secure ePHI that’s included in HIPAA portal invoices, consider the following information.

Who Uses HIPAA-Secure Invoicing?

The need to remain HIPAA compliant adds significant layers to the entirety of eCommerce platforms, including the aspect of invoices. This means that many types of medical billing will be involved with invoicing in some way, all of which can be accessed by a central HIPAA-compliant patient hub or customer account.

HIPAA-compliant billing for medical practices.
HIPAA-compliant medical billing software as a practice management solution.


Pharmacies sell directly to consumers, but they may also sell in bulk to hospitals and other healthcare facilities. This often means a significantly different approach to invoicing for each. Consumers will often be paying out of pocket or providing insurance information. Bulk B2B eCommerce sales will often need delayed payment options.

Healthcare Providers

Medical billing is a huge business, and automated billing via USPS mail has long been the standard. Too many healthcare facilities drag their feet to provide what customers really want: easy to use, easy to pay invoices via a HIPAA-compliant patient portal. Because a single procedure can lead to bills from multiple sources, these invoice portals are an excellent place to consolidate this information.

HIPAA-compliant accounting software works with electronic health records.
Developers providing suitable HIPAA-compliant software may sign a business associate agreement.

Medical Device Providers

Not every prescription is for medicine. Many medical devices can’t be sold directly to the public without doctor approval, and that’s where invoicing for medical devices comes in. Many of these devices can be extremely expensive, and the patient may be splitting the cost with insurance. Payment plans might even be involved, which we’ll talk about below.

Lab Tests

Patient portals and eCommerce platform account pages can also be an excellent way to gather lab results to be paid. Because labs often have many different stages—ordered, scheduled, administered, interpreted, and the doctor meeting to discuss the results with the patient—labs may require invoices if they’re not paid for when administered/performed.

HIPAA-compliant medical billing software can implement electronic health records.
HIPAA-compliant accounting software for a medical practice.

How Invoices Are Interacted With

HIPAA-covered portals can give the user many options to interact with the invoice. Here are some of the most common...though a good developer can make it do whatever your business logic and workflow requires.

  • List of Invoices – A patient might have five invoices from five different doctor’s visits, or they might have five invoices from one visit (i.e., breakout invoices from the doctor visit, lab work, prescriptions, etc.)
  • Pay Multiple Invoices – As we mentioned above, there may be multiple invoices generated from a single visit. Patients have the ability to select and pay multiple invoices at once, saving them time and delivering a better self-service experience.
  • Status of Invoices – The patient will be able to see what invoices have been paid, which ones are pending with insurance, and which ones on which payment still has to be addressed.
  • Filtering – Related to status, filtering can organize invoices in any way a patient likes (and in whatever way you deem appropriate). Filters can be enabled to show open invoices, only those that have been paid, or only invoices from a specialist.
  • Sorting – Sorting can be by date, amount, providers, or any other option you or your customer needs.
  • Detail View – Invoice pages usually start out in list view, giving just enough information to let the patient identify each one. A detail view will give them much more information if they need it.
  • Reorder Items – Quick and easy reordering is a must for any customer. The easiest way to make a sale is to make it easier to order from you than going through the process of finding another vendor.
  • Track Shipments – Any order containing two or more items may be split and shipped separately. Online invoices give the customer the ability to track each shipment individually.
  • Print – Patients may need hard copies to show to doctors or to simply keep themselves organized.

How Invoices Can Be Paid

There are quite a few common ways in which invoices can be paid, because insurance and HIPAA B2B eCommerce can complicate the situation considerably.

HIPAA-compliant billing can work with an insurance company.
  • Immediate Payment – Patients/Customers may simply be paying out of pocket, which usually means paying by credit card.
  • Send Individuals a Bill – You may offer your customers the chance to request a paper copy mailed via USPS if they insist on paying my physical check. While it might not be your preferred method to receive payment, you don’t want to alienate aging customers, since they’re spending more than their younger counterparts.
  • Insurance – Invoices aren’t always paid right away, especially if a customer or patient supplies insurance information. APIs can easily be added to the medical billing platform for private insurance, Medicare, and Medicaid.
  • Recurring Payments – If a person is paying out of pocket or has a considerable amount of the bill left over after insurance has paid, they may need to create a payment plan. You can set minimum amounts they are required to pay each month.
  • Net 30/Corporate Check – Pharmacies and other medical supply companies may be selling to other businesses as well in a B2B fashion. Invoicing will work much the same as with an individual, except that you might allow different billing options for large orders.

Working With A HIPAA Developer

Working with HIPAA and insurance adds levels of complexity that most eCommerce businesses don’t have to deal with. It’s important you find a developer with experience in both fields; the problems they’ve solved in the past can save you grief in your future, whether you're billing an individual or are tackling B2B invoicing.

Clarity has been working on HIPAA-compliant websites, medical apps, and more for over a decade. We have an extensive collection of free HIPAA articles on our site, so we invite you to use those. We also offer a complimentary discover process, where we’ll bring our business analysts and tech people together to create a plan for your HIPAA platform. You can take this plan with you whether you work with us or not, so why not give it a go?



ePHI stands for electronic Protected Health Information, which refers to any individually identifiable health information that is transmitted or maintained in electronic form. This includes information such as medical records, treatment histories, or any data that can identify an individual's health status. It is crucial to protect ePHI during invoicing because of privacy and security concerns.

When processing invoices related to healthcare services, ePHI might be included in the billing details. This could involve patient names, diagnoses, treatment codes, and insurance information. Mishandling or unauthorized exposure of this data can lead to serious consequences, including breaches of patient confidentiality, identity theft, and legal repercussions.

Protecting ePHI during invoicing involves strict adherence to privacy laws like HIPAA (Health Insurance Portability and Accountability Act) to safeguard patient information. Implementing secure billing practices, encryption of data, and limiting access to authorized personnel are essential measures to ensure the confidentiality and integrity of ePHI during the invoicing process.


HIPAA stands for the Health Insurance Portability and Accountability Act, which was enacted in 1996 in the United States. It is a comprehensive federal law designed to protect the privacy and security of patients' medical information. HIPAA is important for healthcare providers because it sets national standards for the protection of sensitive patient health information (PHI) and establishes rules for the use and disclosure of this information.

By complying with HIPAA regulations, healthcare providers ensure that patients' PHI remains confidential and is only shared when necessary for treatment, payment, or healthcare operations. This enhances trust between patients and providers, protects against unauthorized access or breaches, and helps prevent identity theft and fraud related to healthcare information. HIPAA also requires healthcare organizations to implement security measures like access controls, encryption, and training to safeguard patient data, promoting overall data security and integrity within the healthcare industry.


HIPAA-compliant billing software achieves compliance through several key measures.

First, it employs robust encryption protocols to safeguard Electronic Protected Health Information (ePHI) during transmission and storage. Access controls are implemented to ensure that only authorized personnel can view or modify sensitive data.

The software also maintains detailed audit trails, recording all interactions with ePHI for accountability and monitoring purposes. Regular security updates and patches are applied to address potential vulnerabilities promptly.

A Business Associate Agreement (BAA) is established between the software provider and the healthcare entity, outlining their shared commitment to HIPAA compliance. This agreement solidifies the software provider's responsibility for protecting ePHI and sets clear expectations for security measures.


When selecting HIPAA-compliant billing software, several essential features should be prioritized.

  • Robust encryption capabilities are crucial to safeguard Electronic Protected Health Information (ePHI) during both storage and transmission.
  • Access controls ensure that only authorized personnel have the privilege to view or modify sensitive data.
  • The software should also maintain comprehensive audit trails, logging all interactions with ePHI for accountability and monitoring purposes.
  • Regular security updates and patches should be provided to promptly address potential vulnerabilities.
  • A Business Associate Agreement (BAA) with the healthcare provider should be established, affirming the software provider's commitment to HIPAA compliance. This agreement outlines responsibilities and expectations for security measures.
  • Seamless integration with existing systems and user-friendly interfaces can enhance overall workflow efficiency, making the software a valuable asset in the healthcare billing process.

Cloud-based billing software can be HIPAA-compliant, but it requires specific security measures and protocols to meet the stringent standards set by the Health Insurance Portability and Accountability Act (HIPAA).

When considering cloud-based solutions, it's crucial to ensure that the provider offers robust encryption for data at rest and in transit. Access controls must be in place to restrict unauthorized access to Electronic Protected Health Information (ePHI). The cloud service should also have stringent policies for physical and environmental security in their data centers.

Regular security audits, updates, and monitoring processes are essential to maintain compliance. Furthermore, obtaining a Business Associate Agreement (BAA) from the cloud service provider is imperative, as it legally binds them to uphold HIPAA compliance standards.


HIPAA-compliant payment apps are specialized software solutions designed to facilitate secure processing of healthcare-related transactions while adhering to the strict privacy and security standards outlined in the HIPAA regulations. This billing software contains robust accounting features to assist a medical practice with payment processing

These platforms employ encryption, access controls, and other robust security measures to protect sensitive patient information during payment processing.

These apps offer functionalities like online bill pay, electronic statements, and secure payment portals, allowing patients to settle their healthcare bills conveniently and securely. They integrate seamlessly with practice management software, electronic health records (EHRs), and billing platforms.

By using HIPAA-compliant payment apps, healthcare providers ensure that financial transactions are conducted in a manner that safeguards patient privacy and complies with regulatory requirements. This not only fosters trust between patients and providers but also helps avoid potential legal and financial repercussions associated with HIPAA violations.


HIPAA-compliant accounting software plays a critical role in medical billing. HIPAA rules mandate stringent privacy and security standards for handling patients' electronically protected health information (ePHI). In the context of medical billing, this means that any software used must meet HIPAA requirements to safeguard sensitive patient data. This includes HIPAA-compliant payment apps that patients use on their phones.

Using non-compliant software can lead to severe legal consequences and reputational damage for healthcare providers. Violating HIPAA regulations can result in hefty fines, making compliance a non-negotiable aspect of medical billing software.

HIPAA compliance software ensures encryption, access controls, and audit trails are in place to protect ePHI. It also enforces strict authentication protocols, ensuring only authorized personnel can access patient information. This safeguards against data breaches, identity theft, and unauthorized disclosures.

HIPAA-compliant accounting software helps streamline billing processes. It enables accurate and timely claims submissions, reducing the chances of billing errors. This leads to faster reimbursements and improved cash flow for medical practices and other healthcare providers.

HIPAA-compliant accounting software is indispensable in the healthcare industry. It not only safeguards patient privacy but also ensures smooth, efficient, and legally compliant medical billing operations. Choosing such software is an essential step in providing quality care while adhering to HIPAA rules.

Still have questions? Chat with us on the bottom right corner of your screen #NotARobot

Related Posts

Sitefinity developers can make custom widgets for Sitefinity DX.
Stephen Beer is a Content Writer at Clarity Ventures and has written about various tech industries for nearly a decade. He is determined to demystify HIPAA, integration, enterpise SEO, and eCommerce with easy-to-read, easy-to-understand articles to help businesses make the best decisions.