Vulnerability scans are a standard part of most security programs. Love them or hate them, they’re often the first control teams put in place to understand exposure.
But here’s the reality: a vulnerability scan is not a true measure of risk.
Automated scans surface known issues, but they don’t tell you how exploitable those issues really are, how attackers would chain them together, or whether your defenses would actually stop a real attack. Relying on scan results alone can create a false sense of security—especially as cloud, SaaS, and identity-based attack surfaces keep expanding.
This article focuses on the limitations of vulnerability scanning, what scans commonly miss, and how to close those gaps.
TL;DR
Automated vulnerability scans only show part of the risk. They identify known issues, but they don’t validate real-world exploitability or how attackers chain weaknesses across modern cloud, SaaS, and identity environments.
This guide covers:
- What is a Vulnerability Scan
- Limitation of Vulnerability Scan
- How to Uncover Vulnerabilities That a Scan Might Miss
- Vulnerability Scanning vs. Penetration Testing
Want expert-led testing beyond checklists and scans?
What is a Vulnerability Scan?
Vulnerability scans tell us the known vulnerabilities that exist in an organization. It is an automated process that discovers and reports on vulnerabilities in systems, software, and networks.
By looking for exploits or flaws in software, they give you an idea of what vulnerabilities need to be fixed and whether your current patching or update process does a good job of fixing them.
What Are the Limitations of Vulnerability Scanning?
A vulnerability scan only looks for known vulnerabilities—i.e., vulnerabilities that have been reported. Basically, it looks for a marker that a patch or upgrade has been installed.
Key limitations include:
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Patch detection without validation
Scans confirm whether a patch exists, not whether it effectively mitigates the vulnerability or is correctly implemented. -
No real-world attack context
Automated vulnerability scanning does not show how multiple weaknesses could be chained together across identities, applications, and infrastructure. -
Limited cloud and SaaS visibility
Many tools struggle with modern environments, where cloud and SaaS misconfiguration risk often creates more exposure than missing patches. -
No insight into threat actor behavior
Scans do not adapt to modern threat actor behavior, such as identity abuse, token theft, or living-off-the-land techniques. -
Static view of a dynamic attack surface
As cloud resources and access permissions change, scan results quickly become outdated.
What Happens If You Miss a Critical Vulnerability
If you miss a critical vulnerability, it’s a big risk. They can leave critical data and systems exposed to attackers and the public. In turn, malicious actors can use all of this against you to infiltrate your network and compromise your systems and data.
And the cost of a successful exploit is anything but small: Missing a vulnerability could result in business downtime and even millions of dollars of damage to a company. Make sure your cybersecurity incident response plan is ready in case a successful exploit happens.
How to Uncover Vulnerabilities That a Scan Might Miss
Here are four methods our experts at ProArch recommend and use to bring context to a vulnerability scan’s results. Use these next time you perform a vulnerability scan to find threats that may still be lurking.
1. Cross-Reference Vulnerability Scan Results with Threat Intelligence Sources
Threat intelligence sources provide context, real-time information, and insights into the latest tactics, techniques, and procedures (TTPs) employed by threat actors.
These sources offer essential information about the known vulnerabilities and exploits that are actively used by attackers, as well as providing early warning alerts and warnings about emerging threats.
They can help you understand the specific threats that are relevant to your industry, technologies, and geographic location. Using this added context with the vulnerabilities found from a scan enables you to prioritize where to focus for greatest risk reduction.
Here are some threat intelligence sources to consider subscribing to:
- Infraguard
- CISA Automated Indicator Sharing
- AlienVault Open Threat Exchange
- SANS Internet Storm Center
- Cisco Talos Intelligence
2. Manually Inspect Source Code
In the case of a custom application, manual inspection of source code is crucial to identify vulnerabilities. Examining the source code helps identify common vulnerabilities at the code level, such as SQL injection, cross-site scripting (XSS), and security misconfigurations. By manually inspecting the code, you can find vulnerabilities that are specific to an application’s logic and unique features.
3. Open-Source Information Gathering
As we’ve established, analyzing outside of what scans reveal is essential, and that involves open-source information gathered from the dark web, the public web, and brand-related sources.
Information about a company's organizational structure, employee details, technology stack, and data mistakenly accessible to the public is commonly found on the public web. On the dark web, you may find things like employee credentials and specific exploit tools or techniques.
These sources will help reveal if any sensitive or proprietary information has been leaked like employee credentials.
4. Get a Penetration Test
If you're not sure where your security posture stands, investing in penetration testing (pen test) is the best way to identify vulnerabilities and risks in your environment quickly.
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Are there vulnerabilities we don’t know about?
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Are our security investments working?
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Will we pass our next compliance audit?
Penetration testing is a best practice for continuously validating the security controls in place to ensure assets are protected. More specifically, penetration testing services is an exercise where an ethical hacker tests the security measures of a business to identify vulnerabilities and assess the effectiveness of its security defenses.
Vulnerability Scanning vs. Penetration Testing: What’s the Difference?
| Dimension | Vulnerability Scanning | Penetration Testing |
|---|---|---|
| Core Objective | Identify known vulnerabilities across systems, applications, and networks | Simulate real-world attacks to determine what can actually be exploited |
| Method | Fully automated, tool-driven analysis | Human-led testing combined with tools and attacker techniques |
| Type of Findings | Missing patches, outdated software, known CVEs, basic misconfigurations | Exploitable weaknesses, attack paths, privilege escalation, data exposure |
| Context & Correlation | Limited context; findings are isolated and not chained | Full attack context with vulnerabilities chained across systems and identities |
| Exploitability | Assumes risk based on severity scores | Confirms real-world exploitability and business impact |
| Attack Surface Coverage | Primarily infrastructure and known endpoints | Applications, APIs, cloud, identity, SaaS, and hybrid environments |
| Cloud & SaaS Visibility | Often limited; struggles with identity and configuration risk | Strong focus on cloud, SaaS, and identity-driven attack scenarios |
| Threat Actor Simulation | Does not account for modern threat actor behavior | Models how real attackers think, move, and adapt |
| Security Control Validation | Does not test detection, alerting, or response | Actively validates detection, response, and escalation processes |
| Business Impact Insight | Technical findings with limited business context | Clear impact mapping to data exposure, downtime, and compliance risk |
| Frequency | Run continuously or on a schedule | Conducted periodically or after major changes |
| Best Use Case | Baseline visibility and hygiene checks | Deep security posture validation and risk confirmation |
Know your real risk—
before attackers do.
Start Strengthening Your Cybersecurity Posture
Vulnerability scans show what’s known. ProArch helps validate what’s actually exploitable in your cybersecurity environment.
Our penetration testing services go beyond automated findings to simulate real-world attacks across applications, networks, cloud, identity, and SaaS environments. The focus is on real impact, not theoretical risk—so cybersecurity teams know what to fix first and why.
The result is clearer risk visibility, stronger security posture validation, and improved readiness for audits and modern cyber threats.
Explore ProArch’s Penetration Testing Services
