Overcoming Common Challenges in Penetration Testing

Penetration testing is a critical part of any robust security strategy. However, How to Overcome Common Challenges in Penetration Testing is a question many organizations ask as they refine their security programs. New threats, evolving technologies, and organizational constraints can make pen testing complex. This blog post examines common penetration testing challenges and offers concrete strategies to overcome them. We’ll discuss technical, operational, and organizational obstacles that testers face, and present best practices for penetration testing hurdles. By understanding these challenges and implementing proven solutions, teams can ensure their penetration tests remain effective, efficient, and aligned with business needs.

Common Penetration Testing Challenges

Penetration testing faces a variety of hurdles in today’s fast-paced environment. Organizations often cite resource limitations, expertise gaps, and scope complexities as major pain points. Other challenges include evolving threats that outpace testing, poor communication with stakeholders, and stringent compliance requirements. In a 2024 industry survey, 62% of respondents reported that the lack of resources to act on findings or perform remediation was their top challenge. Nearly one-third also struggled with hiring skilled testers or finding qualified third-party vendors (34% each). These findings illustrate the broader cybersecurity skills gap impacting penetration testing roles.

Key challenges include:

• Limited Remediation Resources: Even when tests uncover critical issues, teams often lack time, budget, or personnel to fix them promptly. Without a clear remediation plan, vulnerabilities remain open, reducing the value of the test.
• Skills and Expertise Gaps: A global shortage of experienced pen testers already exists. (ISC)² reports penetration testing as one of the most in-demand yet understaffed skills, Gartner predicts that by 2025 staffing shortages and human failure could contribute to over 50% of major cyber incidents. This makes finding and retaining qualified testers a persistent challenge.
• Scope and Coverage Complexity: Defining what to test – and what not to test – is often difficult. Narrow scopes can miss key assets, while overly broad tests waste time. Regulatory changes have pressured organizations to expand their scope. For example, survey data show 53% of companies broadened their pen test scope last year, up from 29% (Core Security, 2024). Supply chain and third-party risks also drive broader coverage requirements.
• Technical Environment Challenges: Modern environments (cloud, IoT, microservices) introduce unique complications. Misconfigured cloud services and APIs (common in cloud pentesting) can hide vulnerabilities. Rapid deployment cycles and ephemeral assets make it hard to keep up. Legacy systems or custom architectures can be difficult to test comprehensively.
• Tool and Automation Limitations: Relying solely on automated scanners can lead to gaps. Tools may generate false positives or miss business-logic flaws. Automation requires skilled oversight to interpret results correctly. At the same time, manual testing of every component is impractical, so finding the right balance is challenging.
• Poor Communication & Stakeholder Buy-In: Penetration tests can impact operations, so clear communication with IT, management, and legal teams is essential. Misalignment on goals or risk tolerance leads to friction. In some cases, stakeholders view a single test as a “check-box” exercise and are reluctant to invest in follow-up. Indeed, most organizations struggle with a lack of follow-up after testing, as retesting often takes a backseat.
• Compliance and Regulatory Pressure: Many industries face strict security standards. For instance, PCI DSS explicitly requires annual internal and external penetration tests. New regulations like the EU’s NIS2 directive and the upcoming DORA for finance will expand testing requirements. Adapting to evolving compliance landscapes forces teams to run more tests and cover more assets, often without additional resources.

Together, these challenges can severely hamper a testing program’s effectiveness. However, recognizing them is the first step toward overcoming penetration testing obstacles. In the next sections, we present strategies, pen testing challenges, and solutions that security teams can apply to tackle each issue.

How to Overcome Common Challenges in Penetration Testing

Overcoming common challenges in penetration testing involves proactive planning, skill development, and strategic tool use. Below are concrete solutions aligned with the challenges above, each aiming to turn hurdles into strengths. Applying these strategies will help organizations improve their testing outcomes and security posture.

1. Define Clear Scope and Objectives

One root cause of many problems is an unclear scope. To overcome this, all stakeholders should be involved early, and the exact goals should be documented. Clarify what systems, networks, and applications will be tested – and equally important, what is out of scope. By defining objectives and limitations upfront (such as testing internal networks, external apps, or social engineering), teams avoid misunderstandings and rework. For example, a financial firm might specify that all customer-facing cloud services plus on-prem databases are in scope. Clear boundaries help prioritize efforts and prevent testers from going “off course”.

Define success criteria with business owners: will the test target compliance, new features, or known high-risk areas? Having concrete success metrics (like “no critical vulnerabilities unremediated for more than 90 days”) ensures alignment. A detailed scope also aids in selecting the right tools and test types – e.g. including IoT devices or excluding low-risk legacy printers. This clarity overcomes limited time by focusing resources on what matters most.

2. Secure Adequate Time, Budget, and Resources

Acknowledging budgetary constraints is crucial. However, framing pen tests as risk mitigation rather than optional extras can help secure funding. Highlight that timely remediation saves money long-term by preventing breaches. In practice, request dedicated time slots for testing and retesting. For instance, schedule quarterly or biannual tests aligned with development sprints. Use phased approaches if necessary: one sprint for testing, another for fixes.

To cope with limited budgets, consider a mixed model of internal and external resources. A smaller in-house team can handle routine scans and assessments, while third-party experts tackle complex cases. This hybrid approach spreads costs and ensures specialized knowledge when needed. Organizations can also negotiate yearly contracts with pentest firms for retesting at pre-set rates, instead of one-off expensive engagements.

Integrate automated tools to maximize efficiency. For example, schedule weekly vulnerability scans (or “continuous scanning”) to catch trivial issues, reserving expensive manual tests for high-risk changes. This layered strategy (vulnerability scanning as filler between pen tests) ensures that no time is wasted and keeps basic security hygiene up to date. In short, planning and budgeting for testing as an ongoing program, not just a one-off event, is key to surmounting resource constraints.

3. Invest in Training and Expand Expertise

Bridging the skills gap is essential. Organizations can overcome pentesting shortages by training existing staff and building internal skills. For example, cybersecurity analysts can be rotated into penetration testing roles on a part-time basis, supported by vendor tools and training. Use platforms or “cyber ranges” to upskill IT professionals with practical exercises. Encourage certifications (e.g., OSCP, CEH) and regular training budgets.

Partnering with educational institutions or bootcamps can create a pipeline of junior testers. Mentorship is effective: Pair novice testers with senior pentesters on engagements. Internally, share knowledge via documentation and “lessons learned” sessions after each test.

When hiring, focus on problem-solving ability and domain knowledge rather than just credentials. Given the talent scarcity, consider contracting vetted consulting teams if in-house talent isn’t available. However, vet third-party testers carefully: avoid “drive-by” firms offering suspiciously low rates. Look for references, certifications, and proof of methodology. Proper vetting helps avoid fake or unqualified pen testers.

By investing in continuous learning, organizations not only fill roles but build a culture of security expertise. This multi-pronged approach directly addresses the obstacle of expertise.

4. Balance Automated Tools and Manual Testing

Modern pentesting requires both automation for breadth and human insight for depth. To avoid overreliance on one approach, blend tools and manual effort. Use automated scanners and vulnerability management (VM) tools to cover large attack surfaces quickly. These can automatically run outside business hours and flag common issues (e.g., outdated software). However, dedicate time for manual, scenario-based tests where tools fall short: business logic tests, chained exploits, and social engineering.

Regularly update and tune your tools to minimize false positives. A good practice is to review scan results immediately, filter duplicates, and mark critical findings for manual verification. This reduces wasted effort. For web app tests, run automated dynamic scans first, then manual OWASP Top 10 testing. For network tests, use automated port scans, but then try manual exploitation of key services.

Also, adopt continuous penetration testing concepts. New methodologies like CASPT integrate automated tests into development cycles. For instance, run automated tests on every major code commit (via CI/CD pipeline) to catch issues early. Periodically, supplement this with full manual pentests. This approach stays current with an evolving attack surface and ensures that automated tools are aligned with organizational changes.

5. Establish Clear Communication and Reporting

Poor communication can derail pentesting efforts. Overcome this by fostering transparency with all stakeholders. Begin each engagement with a kickoff meeting: IT, legal, management, and testers should understand the plan. Use plain language to explain the test’s purpose and scope to non-technical stakeholders.

During testing, provide interim updates if needed. For example, if a high-impact finding arises mid-test, inform affected teams immediately so they can take short-term mitigations (e.g., disabling a vulnerable port).

After testing, produce actionable reports. A common pitfall is dumping raw findings without context. Instead, prioritize vulnerabilities, describe them in business terms, and recommend specific fixes. (A typical practice is to align severity with business risk, e.g., “This vulnerability could allow data exfiltration” rather than “input validation error.”) Where possible, include proof-of-concept, affected assets, and retest plans.

To tackle the issue of follow-up, requires formal acceptance of remediation plans. For instance, create a tracking sheet listing each finding, the due date for fixes, and the person responsible. Schedule a retest date at the outset. This way, remediation becomes part of the project timeline. Some organizations formalize this in SLAs or post-test workshops to ensure no issue falls through the cracks.

Lastly, consider consolidating vendors. Dealing with one or two pentest providers (rather than many) can simplify communication. It creates a single point of contact and builds familiarity. However, vendor lock-in should be avoided by rotating testers every few years.

6. Embrace Compliance as a Catalyst

While regulations can seem burdensome, they can also drive improvement. Compliance requirements like PCI DSS, HIPAA, and NIS2 mandate regular testing. Use these mandates as justification to secure the budget and schedule. For example, if PCI requires annual penetration tests, align your pentest program timeline with that schedule. Document these regulatory drivers in your project plans – it helps justify the work to leadership.

Use compliance requirements to expand your security practices incrementally. If PCI only requires external pen tests, consider asking for internal network tests as well, since you already have funding on the table. Similarly, many organizations now expand beyond just the audited systems. Recently, many companies have increased the frequency of pen tests and broadened their scope due to compliance changes. While this may strain resources initially, it ultimately strengthens defenses across the enterprise.

Stay updated on evolving laws. For example, GDPR’s impact means testing systems holding EU data, and the upcoming DORA (2025) will pressure financial firms to include more infrastructure. Use industry groups or infosec communities to monitor changes. Proactively adjust testing programs (and budgets) to align with new mandates. By treating compliance as a checklist that also informs real security needs, teams can overcome the obstacle of regulatory demands.

7. Apply a Layered Security Approach

Penetration testing should be one layer in a comprehensive security strategy. Teams can overcome obstacles by integrating pen tests with complementary practices:

• Vulnerability Management (VM): Since pen tests are periodic, use VM tools for continuous coverage. Weekly or monthly scans fill gaps between tests and reduce last-minute issues during pen test windows.
• Threat Intelligence: Feed current threat data into test planning. If phishing scams or new exploits are trending, include them in the testing scope (e.g., simulate social engineering campaigns).
• DevSecOps: Involve security early in development. Conduct shift-left code reviews and automated security testing so that pen tests aren’t fighting an uphill battle against sloppy code.
• Risk Prioritization: Align testing targets with critical assets. Use business impact analysis to focus on what attackers would most likely target. This ensures efforts yield high-value results.

By weaving penetration testing into a “defense in depth” fabric, organizations don’t rely on tests alone. Each layer supports the others, which helps overcome pen-testing obstacles like missed vulnerabilities or limited resources.

Best Practices for Penetration Testing Hurdles

To make the above strategies actionable, here are the best practices to incorporate into your pentesting program. These summarize how to tackle common challenges head-on:

• Conduct Thorough Pre-Test Planning: Involve development, ops, and security teams to outline the test plan. Establish rules of engagement and emergency contacts.
• Maintain an Asset Inventory: Keep an up-to-date map of systems, applications, cloud assets, and connected devices. This minimizes scope confusion.
• Automate Routine Checks: Schedule automated scans for known vulnerability classes (e.g., CVEs). Use orchestration tools to standardize test processes.
• Limit Blast Radius: Use test accounts and make backups to avoid disrupting production. If possible, test in a mirrored environment.
• Focus on Knowledge Sharing: After each test, run a debrief workshop. Create a “knowledge base” of techniques and fixes found.
• Use Metrics and KPIs: Track metrics like the number of vulnerabilities found by severity, time to remediate, and percentage closed after retest. Use these to improve processes.
• Continuously Learn from Incidents: If a breach or near-miss occurs, integrate those learnings into your next pentest (e.g., test the exploited vector).
• Stay Aware of Emerging Threats: Regularly review resources like the OWASP Top Ten or breach reports to keep test scenarios current (external link).

Implementing these best practices for penetration testing hurdles ensures that each test is purposeful, well-scoped, and followed through to completion. For a deeper dive into related topics, see our internal guide on [Vulnerability Management vs. Pen Testing] (internal link) and the NIST SP 800-115 technical guide (external link) on security testing and assessment.

Future-Proofing Your Penetration Testing Program

Looking ahead, penetration testing must adapt continuously. The rise of AI-driven attacks (such as a reported 1,265% surge in phishing emails due to generative AI) and the growth of cloud and IoT mean new vulnerabilities will keep emerging. Security teams can future-proof their programs by:

• Embracing Continuous Testing: Consider moving toward Continuous Attack Surface Penetration Testing (CASPT), which embeds tests into the development lifecycle. This allows near-real-time feedback on security as code changes.
• Integrating Threat Simulation: Regularly use red teaming or breach-and-attack simulations (BAS). This goes beyond pen testing by emulating sophisticated adversaries.
• Leveraging Automation and AI: Advanced tools can help prioritize findings and simulate attacker behaviors. For example, AI-driven scanners can suggest exploit chains, while machine learning can reduce false positives.
• Collaborating Across Teams: Continue breaking down silos. Align pen testing with incident response and security operations so that test findings translate into overall resilience.
• Reviewing Strategy Annually: At least once a year, audit your pentesting program. Assess if test coverage matches your current architecture (e.g., multi-cloud, remote workforce). As new regulations arise, revise plans accordingly.

By staying agile and informed, security teams overcome common penetration testing challenges even as the landscape shifts. In essence, penetration testing should be a proactive, evolving program, not just a one-off event.

Conclusion

Understanding how to overcome common challenges in penetration testing is not just about fixing vulnerabilities — it’s about building a proactive, scalable, and resilient security program. From limited resources and skill shortages to evolving compliance mandates and complex infrastructures, each challenge presents an opportunity to strengthen your defenses.

By clearly defining scope, blending automation with manual expertise, investing in team development, and integrating penetration testing into a broader security strategy, organizations can transform hurdles into measurable gains. Furthermore, treating compliance as a catalyst rather than a constraint ensures that security testing remains timely, relevant, and impactful.

As threats evolve, so must your approach. Make penetration testing a continuous process — not a one-time checkbox — and align it with business goals. In doing so, you not only uncover weaknesses but fortify your security posture for the future.

If you’re serious about enhancing your cybersecurity expertise, start by evaluating your current testing strategy today. The earlier you act, the better prepared you’ll be for the threats of tomorrow.

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