HIPAA Compliance in Software Engineering: 7 Steps You Can’t Skip

Image from pexels.com

If your app handles Protected Health Information (PHI), whether by collecting it, processing it, or storing it, it must meet HIPAA requirements. For companies working in health tech, HIPAA compliance isn’t optional. It’s essential to keep operations running smoothly and avoid legal trouble.

HIPAA can be confusing. Its rules are broad and often open to interpretation. Without clear direction, it’s easy to feel stuck, build inefficient systems, or miss key requirements.

To help you move forward with confidence, we’ve put together a clear guide to HIPAA compliance for software engineering. We will cover how HIPAA compliance applies to your software and the key steps you’ll need to take to become HIPAA compliant when developing software.

What is HIPAA Compliance?

HIPAA (Health Insurance Portability and Accountability Act) is a U.S. federal law that sets strict standards for the privacy, security, and handling of Protected Health Information (PHI). Any organization that creates, stores, processes, or transmits PHI, including healthcare providers, insurance companies, and their service providers, must follow HIPAA requirements.

HIPAA compliance means your organization has implemented the administrative, physical, and technical safeguards needed to protect PHI from unauthorized access, data breaches, or misuse.

Why HIPAA Compliance Matters in Software

If your software handles Protected Health Information, HIPAA compliance isn’t optional, it’s a legal requirement. But beyond avoiding fines, HIPAA plays a critical role in shaping how healthcare software is built and maintained.

Here’s why HIPAA matters for software engineers:

It Dictates How You Handle Sensitive Data

HIPAA sets strict standards for how PHI is collected, stored, transmitted, and disposed of. As an engineer, this means building secure systems from day one — encrypting data, validating input, managing access, and ensuring secure APIs.

Security and Privacy Are Built into the Code

HIPAA isn’t a one-time checkbox. It requires ongoing controls like access logging, breach detection, session timeouts, and secure authentication. These need to be embedded directly into your application logic and infrastructure.

You Need to Think Like a Risk Manager

Every technical decision — cloud storage, logging methods, third-party services — must account for risk. HIPAA expects software to be resilient against both technical failures and malicious attacks, so engineers need to factor in availability, disaster recovery, and incident response from the ground up.

You’re Part of a Legal and Operational Workflow

Whether you’re working for a healthcare provider or a third-party vendor (business associate), your software must support organizational compliance. This includes role-based access, audit readiness, policy enforcement, and documentation.

It Builds Trust

HIPAA compliance isn’t just about avoiding penalties, it’s about building trust with users, patients, and partners. When your software meets HIPAA standards, you signal that your product is reliable, secure, and built for the realities of healthcare.

7 Best HIPAA Compliance Software for 2025
Avoid Penalties with Top-Rated HIPAA Compliance Tools secureslate.medium.com

How to Make Your Software HIPAA Compliant

To bring your software closer to full HIPAA compliance, you can take the following steps:

Step 1: Establish Robust User Authentication

HIPAA mandates that organizations must confirm the identity of anyone attempting to access electronic protected health information (ePHI). In other words, your system needs a reliable way to ensure that only authorized users can log in and view sensitive data.

The challenge? HIPAA doesn’t tell you exactly how to do this. The regulation is intentionally flexible, leaving it up to you to decide on the most effective methods for verifying identity and blocking unauthorized access.

To meet this requirement, consider implementing the following safeguards:

• Multi-Factor Authentication (MFA): Require users to authenticate themselves using two of three distinct types of credentials:
• Something they know (like a password)
• Something they have (like a mobile token or smart card)
• Something they are (like a fingerprint or facial scan)
• Audit Trails and System Logs: HIPAA expects you to track and record access to ePHI. Every login, access attempt, or action involving PHI should be logged so you can detect suspicious activity and maintain accountability.
• Biometric Access Controls: Use biological data such as fingerprints or retina scans as a secure and unique way to grant access to users.

In addition to these, you should enforce strong baseline protections like complex passwords and unique usernames. Combining these strategies builds a layered defense that strengthens the security of your application and aligns with HIPAA expectations.

Step 2: Restrict Access to Your Systems

Under the HIPAA Privacy Rule, you’re required to limit access to Protected Health Information (PHI) as much as possible. This is known as the “minimum necessary” standard, meaning PHI should only be accessed or shared when absolutely essential to complete a specific task.

There’s no one-size-fits-all rulebook for this. Each organization’s data flow is different, so your policies will need to match how your system handles and shares sensitive health data.

Three foundational steps apply across the board:

1. Identify Roles That Require PHI Access
   Determine which individuals or job roles truly need access to PHI to perform their responsibilities.
2. Define What Data Is Needed
   Specify exactly what types of PHI each role should have access to — nothing more.
3. Set Clear Access Conditions
   Establish rules that define when and under what circumstances those roles can access that information.

Once you’ve defined these roles and data needs, put strong access controls in place. Also consider role-based access, permission settings, and continuous monitoring. Make sure you track who is accessing what and when, so nothing slips through the cracks.

HIPAA also requires that you have a documented emergency access procedure, a way to quickly retrieve PHI during unexpected events, like system failures or crises. HIPAA doesn’t prescribe a format, so you’re free to build a procedure that fits your team’s size and structure as long as it ensures secure access in critical situations.

Step 3: Maintain Confidentiality, Integrity, and Availability Controls

HIPAA Security Rule requires your organization to protect the confidentiality, integrity, and availability of all Protected Health Information (PHI) you handle, whether you’re creating it, transmitting it, receiving it, or storing it.

In plain terms, you need to make sure PHI stays private, untouched, and accessible when needed.

To do this, your security strategy must include a mix of technical tools, administrative policies, and procedural safeguards. What that looks like depends on a few key factors unique to your setup:

• The size and complexity of your organization
• Your existing IT systems and their capabilities
• The probability and impact of risks to PHI
• The cost and feasibility of different security options

Once you’ve chosen the right mix of safeguards, make sure everything is documented, not just the measures themselves, but also the actions you take to meet HIPAA security standards. These records (including digital documentation) must be kept for at least six years, starting from either the date they were created or the last date they were in use, whichever is later.

7 Access Control Mistakes You MUST Fix Now!
Fix These Access Control Flaws Before It’s Too Late! secureslate.medium.com

Step 4: Establish Clear Data Disposal Policies

When hardware or media containing Protected Health Information (PHI) is no longer needed, it must be destroyed or erased in a way that completely prevents any future access to that sensitive information.

Your data disposal policies can be tailored to fit your organization’s needs, but they must guarantee that PHI is irreversibly removed and cannot be recovered.

Common methods to achieve this include:

• Destroying paper records by shredding, burning, or pulverizing them until the information is unreadable and impossible to reconstruct.
• Erasing electronic media by clearing, purging, or physically destroying devices through processes like disintegration or incineration, often using specialized software or services.
• Using certified disposal vendors to securely handle and destroy items such as prescription bottles containing PHI.

Before destruction, it’s important to designate secure holding areas for materials awaiting disposal. These locations, such as locked bins or shredding containers, should be clearly marked and accessible only to authorized personnel.

By carefully managing data disposal, you help prevent accidental leaks and maintain HIPAA compliance.

Step 5: Draft Comprehensive Business Associate Agreements

If you’re a software developer, you may either act as a business associate to a covered entity or partner with other associates in creating parts of your solutions. In both scenarios, it’s crucial to understand Business Associate Agreements (BAAs) and the HIPAA requirements that govern them.

By law, covered entities and business associates must enter into a formal, written contract outlining their responsibilities. While the specifics vary depending on the nature of the collaboration, certain key components are standard in every BAA:

• Clear definitions of how the business associate is permitted to use and disclose Protected Health Information (PHI).
• A provision that prohibits the business associate from using or sharing PHI beyond the terms agreed upon in the contract.
• Obligations for the business associate to comply with HIPAA Security Rule by implementing appropriate safeguards to protect PHI.
• Requirements ensuring the business associate handles PHI in line with HIPAA Privacy Rule, meeting the same regulatory standards as the covered entity.

Having a thorough, well-structured BAA is essential to maintaining compliance and protecting sensitive health information across your software partnerships.

Step 6: Develop an Effective Incident Response Plan

HIPAA mandates that organizations establish and maintain effective policies and procedures to manage security incidents, aiming to minimize their impact swiftly and efficiently.

To comply, your organization must craft a comprehensive incident response plan designed to:

• Detect security threats early
• Contain and resolve incidents quickly
• Document and report incidents thoroughly

For your plan to be effective, it should include:

• Clear assignment of roles and responsibilities for all personnel involved in incident handling
• Up-to-date contact details for every team member engaged in the response process
• Well-defined response procedures and protocols
• A communication strategy outlining internal and external reporting channels
• Standardized protocols tailored to address common threats specific to your organization

If you function as a business associate, HIPAA requires you to notify the covered entity of any data breach within 60 days of discovering it. Your report should detail the incident’s nature and identify the individuals affected, enabling the covered entity to fulfill its reporting obligations promptly.

A thorough incident response plan not only safeguards sensitive information but also ensures regulatory compliance in critical moments.

Step 7: Establish a Comprehensive Contingency Plan

While cybersecurity incidents pose significant risks to Protected Health Information (PHI), HIPAA Security Rule recognizes that other hazards, such as system failures, vandalism, and natural disasters, can also jeopardize sensitive data. To address these broader threats, a contingency plan is essential.

Unlike an incident response plan, which primarily targets cyberattacks, a contingency plan focuses more heavily on safeguarding data from physical and environmental dangers. Together, these plans create a resilient defense against the majority of risks to PHI.

HIPAA outlines five key components for a contingency plan:

• Data Backup Plan: Procedures to regularly back up data to prevent loss.
• Disaster Recovery Plan: Steps to restore systems and data after a disruptive event.
• Emergency Mode Operation Plan: Processes to maintain critical functions during emergencies.
• Testing and Revision Procedures: Regular evaluation and updates to ensure the plan’s effectiveness.
• Applications and Data Criticality Analysis: Assessment of which systems and data are vital for operations.

The first three components are mandatory and must be implemented without exception. The latter two are considered “addressable,” meaning you must apply them if they are reasonable and suitable for your organization. If not, you must document why and adopt alternative measures that provide comparable protection.

A well-crafted contingency plan, combined with an incident response strategy, fortifies your defenses against a wide range of potential disruptions to PHI security.

HIPAA Security Rule: Are You Compliant or at Risk?
Stay Audit-Ready with These Security Practices secureslate.medium.com

HIPAA-Compliant Software with SecureSlate

SecureSlate offers a comprehensive trust management platform that automates up to 85% of the evidence collection required to prove HIPAA compliance. By streamlining your compliance processes, SecureSlate helps your security and compliance teams operate more efficiently, saving valuable time and effort.

Designed specifically with healthcare software developers in mind, SecureSlate’s HIPAA-focused solution supports adherence throughout the entire development lifecycle. The platform boasts a suite of powerful features, including:

• Expert technical and personalized guidance to meet HIPAA mandates
• Simplified inventory management to keep track of assets and data flows
• Automated access reviews to ensure only authorized personnel handle PHI
• A policy builder equipped with HIPAA-specific templates for easy documentation

With SecureSlate, achieving and maintaining HIPAA compliance becomes a smoother, faster journey, empowering your team to focus on innovation while confidently managing regulatory requirements.

Conclusion

HIPAA compliance is more than just a legal requirement, it’s a fundamental part of building secure, trustworthy healthcare software. Following the key steps outlined in this guide helps ensure your app protects sensitive health data while supporting smooth operations and regulatory readiness.

Though navigating HIPAA can feel complex, leveraging tools like SecureSlate can simplify the process by automating evidence collection and compliance management.

With the right approach, your development team can focus on innovation while confidently meeting HIPAA standards and safeguarding patient information.

Ready to Streamline Compliance?

Building a secure foundation for your startup is crucial, but navigating the complexities of achieving compliance can be a hassle, especially for small teams.

SecureSlate offers a simpler solution:

• Affordable: Expensive compliance software shouldn’t be the barrier. Our affordable plans start at just $99/month.
• Focus on Your Business, Not Paperwork: Automate tedious tasks and free up your team to focus on innovation and growth.
• Gain Confidence and Credibility: Our platform guides you through the process, ensuring you meet all essential requirements, and giving you peace of mind.

Get Started in Just 3 Minutes

It only takes 3 minutes to sign up and see how our platform can streamline your compliance journey.