How to Conduct a Comprehensive Cybersecurity Audit for Your SaaS Company
Alexander Sverdlov
Security Analyst
Cybersecurity isn't optional for your SaaS company. It's essential. We will walk you through conducting a thorough cybersecurity audit covering your APIs, cloud infrastructure, and web applications, the same way we would run it for you.
Why Conduct a Cybersecurity Audit?
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Identify vulnerabilities before attackers do.
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Ensure compliance (GDPR, SOC 2, ISO 27001, NIST 800-53, NIST 800-171).
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Maintain customer trust by securing data.
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Prevent expensive breaches and downtime.
- Most importantly: SELL MORE! Yes, you read that right. You will sell more easily to your B2B clients if you present your security measures well.
Step 1: Preparation and Scoping
Now that you've found your auditing partner, it's time to do some prep work. If your team is already busy with daily tasks, you'll have to inform them that they will have to prioritize the audit activities for a week - and let them be slightly less productive during that time. Promise pizza if you have to!
1.1 Define Audit Objectives Clearly
Start with specific goals:
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Identify vulnerabilities in web applications.
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Secure API endpoints.
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Strengthen cloud security configurations.
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Validate compliance requirements.
One benefit few are aware of: during the audit, all the interviews with your team will act as a training exercise, or a consulting exercise. By asking questions and then discussing them, our auditors act as security coaches, explaining why the question is asked and what the benefit is in implementing a particular security control.
1.2 Inventory of Assets
List all systems:
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Web Applications
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APIs (internal and external)
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Cloud infrastructure (AWS, Azure, GCP)
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Databases and data stores
Use tools like:
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AWS Config, Azure Resource Graph, Google Cloud Asset Inventory
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Automated discovery tools (nmap, assetfinder)
After you feel like you've listed everything, send an email to everyone in the company asking them to list the cloud systems and websites they use for work, the email used (personal or corporate) and the admin user on the tool they use.
That is where you will see your biggest surprise. You will find out that suddenly your attack surface has increased ten-fold (well, it was always that large, you just didn't know!).
Step 2: API Security Audit
2.1 Identify and Map all internal and external APIs
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Catalog all API endpoints (internal/external).
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Identify API gateways and authentication mechanisms.
These will have to be discussed with the development team during the audit - we have a special checklist that we go through.
2.2 Review Authentication and Authorization
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Test API keys, JWT tokens, OAuth.
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Confirm least privilege principle.
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Check for exposed credentials.
Tools:
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Postman, Burp Suite, OWASP Zap
2.3 Test for Common API Vulnerabilities
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Injection attacks (SQL, NoSQL).
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Broken authentication (JWT manipulation, API keys).
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Excessive data exposure.
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Improper rate limiting and lack of resource restrictions.
Example Checks:
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Attempt SQL injection using payloads in request parameters.
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Try bypassing authentication by modifying JWT tokens.
Step 3: Cloud Infrastructure Security Audit
3.1 Assess Cloud Account Security
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Audit IAM policies, roles, and access keys.
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Implement multi-factor authentication (MFA).
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Rotate access keys regularly.
3.2 Check Resource Misconfigurations
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Exposed S3 buckets, storage blobs.
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Publicly accessible databases.
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Improperly configured security groups or firewall rules.
Tools:
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AWS Security Hub, Azure Security Center, GCP Security Command Center
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Open-source tools: Scout Suite, Prowler
3.3 Review Logging and Monitoring
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Enable comprehensive logging (AWS CloudTrail, Azure Monitor, GCP Stackdriver).
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Confirm alerts for suspicious activities (e.g., multiple failed logins).
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Ensure log integrity and retention.
Step 4: Web Application Security Audit
4.1 Web Application Mapping
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Identify all web domains and subdomains.
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Enumerate application structure and entry points.
Tools:
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assetfinder, OWASP Amass, Burp Suite
4.2 Vulnerability Scanning and Testing
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Conduct automated scans with OWASP Zap or Burp Suite.
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Manual testing for complex vulnerabilities:
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Cross-site scripting (XSS)
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Cross-site request forgery (CSRF)
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Server-side request forgery (SSRF)
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Directory traversal
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4.3 Session Management and Authentication Checks
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Check session expiry.
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Test multi-factor authentication mechanisms.
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Verify password complexity and storage.
Example:
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Try session hijacking by intercepting and replaying session cookies.
Step 5: Data Security and Encryption Audit
5.1 Identify and Classify Sensitive Data
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Customer Personally Identifiable Information (PII)
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Financial data
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Intellectual property and business-critical information
Action:
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Conduct a thorough data classification exercise.
5.2 Assess Data Encryption Standards
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Verify data encryption at rest (AES-256 recommended).
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Confirm data encryption in transit (TLS 1.2+).
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Inspect encryption key management (KMS, Azure Key Vault).
Tools:
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AWS Inspector, Azure Security Center, Google Cloud DLP
5.3 Evaluate Data Backup and Recovery
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Ensure backups are regular, encrypted, and tested.
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Test disaster recovery processes periodically.
Step 6: Compliance and Regulatory Audits
6.1 Identify Applicable Regulations
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GDPR, SOC 2, ISO 27001, HIPAA
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Clearly document applicable regulatory requirements.
6.2 Audit Compliance Controls
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Review policies, procedures, and documentation.
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Test technical compliance measures (e.g., data anonymization, access controls).
Example Checks:
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Verify GDPR data subject access request handling.
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Confirm SOC 2 evidence and documentation.
Step 7: Reporting Audit Findings
7.1 Organize and Prioritize Findings
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Categorize risks by severity (high, medium, low).
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Clearly detail vulnerability description, risk impact, and recommendations.
Example Report Structure:
| Vulnerability | Risk Level | Impact | Recommended Action |
|---|---|---|---|
| Exposed S3 bucket | High | Data breach risk | Restrict public access immediately |
| Outdated TLS protocol | Medium | Possible interception risk | Upgrade to TLS 1.2+ immediately |
7.2 Present Audit Results Clearly
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Schedule a dedicated meeting with stakeholders.
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Use visuals and concise summaries to highlight critical points.
Step 8: Creating Actionable Remediation Plans
8.1 Assign Clear Responsibilities
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Assign specific team members to each remediation task.
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Clearly set deadlines and follow-ups.
Example Remediation Plan:
| Task | Assigned To | Deadline |
| Update IAM policies | Security Team | 7 days |
| Patch web application vulnerabilities | Dev Team | 14 days |
8.2 Continuous Improvement
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Regularly schedule follow-up audits.
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Continuously update and refine security policies based on findings.
Step 9: Implement Continuous Monitoring
9.1 Set Up Real-time Monitoring
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Integrate SIEM tools (Splunk, ELK, Datadog).
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Enable alerts for critical events (breaches, unauthorized access).
9.2 Regularly Review Security Metrics
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Failed login attempts
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Access from unusual locations
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Changes in system configurations
Cybersecurity audits for your SaaS company aren't a one-time activity-they're an ongoing process. Regularly updating your audit procedures ensures that your company remains secure, compliant, and resilient against emerging threats.
Stay proactive, stay secure!
See also: Is Your SOC 2 Report Useless in Singapore? The 3 Security Gaps That Make Local Banks Reject Your SaaS
Alexander Sverdlov
Founder of Atlant Security. Author of 2 information security books, cybersecurity speaker at the largest cybersecurity conferences in Asia and a United Nations conference panelist. Former Microsoft security consulting team member, external cybersecurity consultant at the Emirates Nuclear Energy Corporation.