Step-by-Step: How to Run API Penetration Tests Using Automated Scanners

Now, a large number of modern applications are either built using APIs or have APIs. But the problem is that they still use outdated manual testing methods that do not have the capacity to catch the threats modern applications are facing.

That’s the reason why API Penetration with Automated Scanners is no longer optional for developers and security teams. We will dive into a step-by-step guide on how it works and why you need it now.

Why APIs Need a Different Kind of Security Testing

Unlike traditional web apps, APIs require a specialized security approach because manual tools can only perform surface-level scans and are not likely to detect runtime-level threats that cause Broken Object Level Authorization, Improper Rate Limiting, and Insecure Endpoints.

Most likely, manual testing can take too much time to find vulnerabilities, and many times they may miss them because APIs are often created by default without the awareness of internal teams. This is where automated API security comes in, as it provides in-depth scanning in very little time and helps developers mitigate risks without missing anything. That's why APIs need different kinds of security testing.

Step-by-Step: How to Use Automated Scanners for API Testing

1. Set the Prerequisites

Before you scan anything, define what you’re testing and why. That means:

• Clearly identifying which APIs are in scope (REST, SOAP, GraphQL)
• Specifying the access level to test with (public, internal, or authenticated)
• Gathering API definitions like OpenAPI/Swagger files or Postman Collections
• Understanding how the API works—its data flow, endpoints, and business logic

Whether you're aiming to uncover security gaps or meet compliance, clear goals are key.

2. Select the Right Scanner

Not all scanners are created equal. Choose one that:

• Supports the protocols and formats you use (e.g., REST, GraphQL)
• Integrates easily into your CI/CD workflows
• Performs dynamic analysis (DAST) to uncover real-world attack vectors

Compatibility and automation are non-negotiable when scanning modern APIs at scale.

3. Configure the Scanner

Now it’s time to set things up. Configuration usually involves:

• Importing your API specs or Postman Collections
• Providing authentication credentials or tokens
• Adjusting scanning policies (e.g., targeting specific endpoints or excluding sensitive ones)

4. Run the Automated Scans

With everything configured, launch the scan. A capable tool will:

• Automatically discover and catalog all active APIs
• Perform both authenticated and unauthenticated scans
• Use fuzzing, active scanning, and passive scanning to detect threats

These tests reveal vulnerabilities like broken authentication, injection flaws, and resource abuse all aligned with the OWASP API Top 10.

5. Review Reports and Plan Remediation

Once the testing is complete, an automated API security scanner generates a detailed report that includes:

• A list of discovered vulnerabilities
• Severity ratings and potential impact
• Contextual details for developers

These reports serve as an actionable roadmap, helping teams prioritize what to fix first and communicate clearly with engineering and security stakeholders.

Common Vulnerabilities These Scanners Catch

Modern API security testing can effectively uncover vulnerabilities such as:

BOLA (Broken Object Level Authorization): Accessing someone else’s data via ID tampering.

Mass Assignment: Manipulating hidden parameters through JSON payloads.

Insecure Authentication Flows: Poor session handling or missing token validations.

Improper Rate Limiting: APIs that can be brute-forced or spammed.

These aren’t just theoretical, these are the same vulnerabilities used in real-world breaches.

Why This Matters to Dev and Security Teams

Security isn’t just a final-stage task anymore. DevSecOps principles demand continuous, automated testing that fits into fast development cycles.

By integrating automated API scanners:

• Devs can find and fix issues early (before production)
• Security teams get broader visibility with fewer manual bottlenecks
• Organizations reduce exposure to high-impact API attacks

Conclusion

Since modern applications are highly API-based, automated API penetration testing is no longer a second guess, because it's faster, efficient, and finds threats beyond surface-level vulnerabilities.

Following the above-mentioned tests, development and security teams can detect vulnerabilities at an early stage, reduce the need for human effort, and build more secure applications.