Summary

It’s important to understand that SOC 2 does not replace HIPAA compliance. They are complementary frameworks. HIPAA is legally mandated for any company handling PHI, while SOC 2 is a voluntary but commercially essential certification. This is where most healthcare software companies underestimate the effort. SOC 2 requires not just implementing controls, but documenting them in a way auditors can verify. You’ll need: - Treating SOC 2 as a one-time project: Certification requires ongoing maintenance, annual audits, and continuous evidence collection

SOC 2 for Healthcare Software: A Complete Guide to Getting Certified

Healthcare software companies face a unique compliance challenge. You need to satisfy HIPAA requirements to handle protected health information (PHI), but many enterprise customers and health systems also require SOC 2 certification before they’ll sign a contract. Understanding how to pursue SOC 2 for healthcare software — and how it intersects with your existing HIPAA obligations — can save you months of confusion and thousands of dollars in wasted effort.

This guide walks you through exactly what you need to know to get SOC 2 certified as a healthcare software company.

What Is SOC 2 and Why Do Healthcare Software Companies Need It?

SOC 2 (System and Organization Controls 2) is an auditing framework developed by the American Institute of Certified Public Accountants (AICPA). It evaluates how your organization handles customer data based on five Trust Services Criteria: Security, Availability, Processing Integrity, Confidentiality, and Privacy.

For healthcare software companies, SOC 2 matters for several reasons:

Enterprise sales requirements: Hospitals, health systems, and large clinics increasingly require SOC 2 reports before vendor onboarding
Investor confidence: SOC 2 signals operational maturity to investors and acquirers
Competitive differentiation: Certification sets you apart from non-certified competitors in a crowded market
Risk reduction: The process forces you to identify and close real security gaps

SOC 2 Type I vs. Type II: Which One Do You Need?

Before starting the process, you need to choose the right report type.

SOC 2 Type I

A Type I report evaluates whether your security controls are designed appropriately at a single point in time. It’s faster to obtain (often 2–4 months) and is useful for early-stage companies that need to show customers something quickly.

SOC 2 Type II

A Type II report evaluates whether your controls actually operated effectively over a defined observation period, typically 6–12 months. Most enterprise healthcare customers will require Type II because it demonstrates sustained, real-world performance rather than a snapshot.

Recommendation for healthcare software companies: If you’re pre-sales or in early growth, start with Type I to unlock deals quickly. Plan for Type II within 12–18 months as you scale.

The 5 Trust Services Criteria: What Healthcare Software Must Address

Most healthcare SaaS companies pursue SOC 2 with at least the Security criteria (required) plus Confidentiality and Availability, since these directly relate to PHI handling and uptime expectations in clinical environments.

Security (Required)

Covers access controls, encryption, vulnerability management, and incident response. This is the foundation of every SOC 2 audit.

Availability

Critical for healthcare software where downtime can impact patient care. You’ll need to demonstrate uptime SLAs, disaster recovery plans, and monitoring infrastructure.

Confidentiality

Addresses how sensitive data — including PHI — is protected, labeled, and disposed of. This overlaps significantly with HIPAA’s technical safeguards.

Privacy

If your software collects data directly from patients or end users, the Privacy criteria may apply. This aligns closely with HIPAA’s Privacy Rule requirements.

Step-by-Step: How to Get SOC 2 for Healthcare Software

Step 1: Define Your Scope

Determine which systems, infrastructure, and personnel are in scope for the audit. For healthcare software, this typically includes:

Your cloud infrastructure (AWS, Azure, GCP)
Application code and databases storing PHI
Third-party integrations (EHR systems, billing platforms)
Internal tools used to access production environments

Keeping scope narrow reduces cost and complexity. Work with your auditor early to align on boundaries.

Step 2: Conduct a Readiness Assessment

A readiness assessment identifies gaps between your current state and SOC 2 requirements. Think of it as a pre-audit audit. You can conduct this internally or hire a consultant. Key areas to review include:

Access control policies and procedures
Encryption standards (in transit and at rest)
Vulnerability scanning and patch management
Vendor management and Business Associate Agreements (BAAs)
Incident response and breach notification procedures
Employee security training and background checks

Step 3: Build and Document Your Controls

This is where most healthcare software companies underestimate the effort. SOC 2 requires not just implementing controls, but documenting them in a way auditors can verify. You’ll need:

Information Security Policy: Your master security governance document
Access Control Policy: Who can access what, and how access is granted and revoked
Change Management Policy: How code and infrastructure changes are reviewed and deployed
Incident Response Plan: Steps for detecting, containing, and reporting security incidents
Business Continuity and Disaster Recovery Plan: How you maintain availability during disruptions
Vendor Management Policy: How you vet and monitor third-party providers

For healthcare software, your HIPAA policies and SOC 2 policies should be aligned and cross-referenced to avoid duplication and contradiction.

Step 4: Implement Supporting Evidence Collection

Auditors don’t just read your policies — they verify them with evidence. Set up systems to collect:

Access logs and user provisioning records
Penetration test results
Security awareness training completion records
Vulnerability scan reports
Change management tickets
Backup and recovery test results

Tools like Vanta, Drata, or Secureframe can automate much of this evidence collection and are popular among healthcare SaaS companies.

Step 5: Choose a Qualified CPA Auditor

SOC 2 audits must be performed by a licensed CPA firm. Not all auditors have healthcare experience, so look for firms familiar with:

HIPAA/HITECH requirements
Cloud-native infrastructure (especially if you’re AWS or Azure-heavy)
SaaS business models

Expect to pay $15,000–$50,000 for a Type II audit depending on scope, company size, and auditor reputation.

Step 6: Complete the Audit and Receive Your Report

During the audit, your auditor will review documentation, interview key personnel, and test controls. For Type II, they’ll also review historical evidence from your observation period.

After the audit, you’ll receive a SOC 2 report containing the auditor’s opinion, a description of your system, and details of any exceptions or findings. Share this report (under NDA) with prospective customers to satisfy their vendor security requirements.

How SOC 2 and HIPAA Overlap for Healthcare Software

One of the biggest advantages for healthcare software companies is that HIPAA compliance work directly supports SOC 2 readiness. Many controls overlap:

Control Area	HIPAA Requirement	SOC 2 Criteria
Access controls	Technical Safeguards	Security
Audit logging	Technical Safeguards	Security
Encryption	Technical Safeguards	Security / Confidentiality
Incident response	Breach Notification Rule	Security
Vendor management	Business Associate Agreements	Security
Risk assessment	Risk Analysis requirement	Security

If you’ve done HIPAA compliance properly, you’re likely 40–60% of the way to SOC 2 readiness before you start.

Common Mistakes Healthcare Software Companies Make

Skipping the readiness assessment: Jumping straight to an audit without understanding gaps leads to expensive findings and delays
Over-scoping the audit: Including systems that don’t need to be in scope inflates cost and complexity
Underdocumenting controls: Having a firewall isn’t enough — you need written policies, configuration standards, and evidence it’s monitored
Treating SOC 2 as a one-time project: Certification requires ongoing maintenance, annual audits, and continuous evidence collection
Misaligning HIPAA and SOC 2 policies: Contradictory documentation creates confusion for auditors and internal teams

Frequently Asked Questions

How long does it take to get SOC 2 certified as a healthcare software company?

Type I certification typically takes 2–4 months from readiness assessment to report. Type II requires an observation period of 6–12 months on top of preparation time. Budget 9–18 months total for a first-time Type II certification.

Does SOC 2 replace HIPAA for healthcare software?

No. HIPAA is a legal requirement for any company handling PHI. SOC 2 is a voluntary certification that demonstrates security maturity to customers. You need both. The good news is they complement each other significantly.

How much does SOC 2 certification cost for a healthcare SaaS company?

Total costs vary widely. Expect $15,000–$50,000 for the audit itself, plus internal staff time, compliance tooling ($10,000–$30,000/year), and any remediation work needed before the audit. Early-stage companies often spend $50,000–$100,000 total for their first Type II certification.

Can we use our HIPAA policies for SOC 2?

Some HIPAA policies map directly to SOC 2 requirements, but you’ll likely need additional policies and controls that HIPAA doesn’t require — particularly around change management, software development lifecycle (SDLC), and vendor risk management.

What happens if our SOC 2 audit finds exceptions?

Exceptions (findings) aren’t automatically disqualifying. Minor exceptions with clear remediation plans are common in first-time audits. Your auditor will describe the exception and its potential impact in the report. Significant or pervasive exceptions can undermine customer confidence, which is why readiness work matters.

Start Your SOC 2 Journey with Ready-to-Use Compliance Templates

Building SOC 2 policies from scratch is time-consuming, expensive, and easy to get wrong — especially when you’re also managing HIPAA obligations. Our professionally written, audit-ready compliance template bundles are designed specifically for healthcare software companies pursuing SOC 2 certification.

Each template is:

Written by compliance experts with healthcare SaaS experience
Mapped to both SOC 2 Trust Services Criteria and HIPAA requirements
Customizable for your specific environment and team size
Ready to hand directly to your auditor

Stop spending weeks writing policies when you could be building your product. Browse our SOC 2 template library and get audit-ready in days, not months.