Web Application Penetration Testing Explained

web application penetration testing

Updated April 12, 2025

Having a robust cybersecurity program is essential for any organization. Fortifying defenses and being as proactive as possible in thwarting cyberattacks are standard in the security realm. But how do you know how well you’re doing? To understand this, you need to test your defenses. One of the best ways to do that is with penetration testing.

What Is Web Application Penetration Testing?

Web application penetration testing is a type of ethical hacking where a simulated attack occurs in an attempt to access sensitive data. It assesses the architecture, design, and configuration of your web applications. Web applications include anything delivered over the internet through a browser interface. As a result, they are the most targeted by cybercriminals.

The objective is for you to identify vulnerabilities before hackers do. It’s an essential part of a health check of your systems.

Access Levels for Web Application Penetration Testing

Every penetration test includes a level of access. The three segments are:

  • Black Box Penetration Testing: In this scenario, testers don’t know the target system’s internal structure. They play the role of a hacker, seeking to find any weakness to exploit.
  • Gray Box Penetration Testing: At this level, the test participants have some general information about the target system. They may know about data structures, algorithms, or codes, and they may also have credentials. Penetration objectives here are slightly different and can involve specific test cases to determine the system’s security.
  • White Box Penetration Testing: The third option enables pen testers to access systems and artifacts like source code and containers. Additionally, they may be able to enter servers running the system.

Web application testing uses both Black and Gray Box Testing. For a comprehensive view of your system’s security, start with the Black Box and then move to the Gray Box. Here’s how they both work.

Black Box Web Application Penetration Testing

With Black Box, this situation emulates the most realistic hacker experience. The testers wear their hacker hats and copy what an actual cybercriminal would do. Those steps involve reconnaissance, finding vulnerabilities, and breaking into your network. Remember that testers have no context about your system, only URLs.

Gray Box Web Application Penetration Testing

In Gray Box, your partners will test each system in scope. At this point, testers have “user” knowledge and system access. The Gray Box Penetration Test approach focuses on an application with multiple users. It will test authenticated users with various roles to ascertain whether someone could escalate privileges, including:

  • Horizontal Privilege Escalation: Tester will attempt, as an authenticated user, to retrieve another user’s data. Someone could do this if the URL is part of the person’s account. For example, you have an application where every user has a unique account number. That account number is part of the URL on the page where the data lives. If you change a number in the URL, the user may be able to obtain entrance into another account.
  • Vertical Privilege Escalation: In this exercise, an authenticated user will attempt to assume administrator-level access. A tester could accomplish this if a web application uses a value to represent a username in a hidden field, which returns with successful authentication. A tester would then try to change the value from “username” to “root” or “administrator” to attain that privilege level.

This information provides insight into how a group performs the tests. Another key component of web application pen tests is the OWASP (Open Worldwide Application Security Project) Top 10.

What Is the OWASP Top 10, and Why Does It Matter in Pen Testing?

OWASP is a nonprofit organization that aims to improve software security. Its top 10 is a standard awareness document that developers, cybersecurity professionals, and other security stakeholders can use as a guide. The top 10 is a broad consensus of the most critical risks to web applications. The latest version, from 2021, consists of these categories.

  1. Broken Access Control: Access control comes from policies about how a user can operate within an application based on intended permissions. Failures here can cause unauthorized information disclosure, modification, or destruction. The most Common Weakness Enumerations (CWEs) map to this more than any other category.
  2. Cryptographic Failures: In this category, you’re looking for how protected data is in transit and at rest, including passwords, PHI (protected health information), intellectual property, data that falls under privacy laws, and credit card numbers.
  3. Injection: In Injection, testers would consider an application vulnerable to attack if it doesn’t validate, filter, or sanitize user-supplied data. The application would also check for hostile data.
  4. Insecure Design: This was a new category in 2021. It’s a broad category of various weaknesses deemed “missing or ineffective control design.” It focuses on design flaws, not the implementation of the system.
  5. Security Misconfiguration: A misconfigured application can be a way in for hackers. As part of the penetration test, testers would look for these signs, such as missing appropriate security hardening, enabling unnecessary features, keeping default accounts and passwords active, handling errors, and more security settings.
  6. Vulnerable and Outdated Components: These are known issues that can be difficult to test and discern risk. Testers will locate these risks if they learn that organizations don’t know all the versions they have running, are using unsupported and out-of-date software, haven’t completed fixes or upgrades, or aren’t testing compatibility.
  7. Identification and Authentication Failures: Applications should confirm a user’s identity, authentication, and session management. Authentication weaknesses may be present if the application permits credential stuffing, brute force, automated attacks, weak or default passwords, a lack of multifactor authentication, or other authentication failures.
  8. Software and Data Integrity Failures: This type of failure refers to code and infrastructure that doesn’t protect against integrity violations. For example, some plugins or modules may be from an untrusted source. If so, there is trouble in the CI/CD (continuous integration/continuous delivery) pipeline. As a result, there could be unauthorized access, malicious code, or system compromise.
  9. Security Logging and Monitoring Failures: Most organizations find testing security logging and monitoring challenging. This category focuses on detection, escalation, and response to active breaches. Insufficient activity here can impact your ability to identify and respond.
  10. Server-Side Request Forgery (SSRF): An SSRF flaw happens when web applications fetch a remote resource and don’t validate the user-supplied URL. An attacker could manipulate the application to send a crafted response to an unexpected destination, even with firewalls, VPNs, or other barriers in place.

As you can see, the OWASP Top 10 covers a wide range of web application risks. It’s critical that they are part of your pen tests. In addition, there are other common web application issues that your pen test provider should cover. Those categories include different types of injection (e.g., SQL, OS command, server-side code, server-side template, etc.), server-level issues, and other manipulations.

These pen tests are extensive and include seven steps.

The Seven Steps of a Web Application Pen Test

A web application pen test should include these seven phases:

  1. Planning and Preparation: Pen-test teams gather information and plot out their attack strategy.
  2. Reconnaissance/Discovery: Ethical hackers are investigating and collecting data on the target system. Scanning of systems occurs here.
  3. Vulnerability Enumeration/Analysis: Testers conduct a vulnerability assessment to identify weaknesses.
  4. Initial Exploitation: After reviewing the results from the assessment, pen testers use techniques to validate, attack, and exploit.
  5. Expanding Foothold/Deeper Penetration: After the initial infiltration, testers will strive to go further with escalation.
  6. Cleanup: Testing parties retreat from the application and return it to its former state.
  7. Report Generation: Your provider creates a comprehensive analysis of the pen tests with details on weaknesses and vulnerabilities and remediation recommendations.

Pen tests for your web applications deliver so much valuable information. Let’s look at the benefits of using these.

The Benefits of Web Application Penetration Tests

Penetration testing’s most valuable advantage is that ethical hackers find your weaknesses before the real ones do. It’s a way to improve your cybersecurity measures and be as proactive as possible in thwarting cyberattacks. Additionally, it provides these benefits:

  • It can support your compliance program and adherence to regulations. For healthcare organizations, you can exceed the expectations of HIPAA with pen tests.
  • You can better assess your infrastructure. Your firewalls and DNS servers are public-facing, and any information adjustments can leave your system vulnerable. Get insights on this before hackers find them.
  • You can fix problems within web applications. You may have been unaware of them or not made them a priority. The remediation plan will advise you on what to do.
  • It can confirm security policies and if they’re effective.

Ready to realize all these benefits and more? Learn about our web application pen testing services and how we can help today.

Web Application Penetration Testing FAQs

Please schedule a 30-minute Discovery Session with us so we can best understand your objectives.

Penetration testing, also known as security testing, should be conducted on a regular basis to ensure the protection of organizations' digital assets. It is generally recommended that all organizations schedule security testing at least once a year. However, it is essential to conduct additional assessments in the event of significant infrastructure changes, prior to important events such as product launches, mergers, or acquisitions.

For organizations with large IT estates, high volumes of personal and financial data processing, or strict compliance requirements, more frequent pen tests are strongly encouraged. Such organizations should consider conducting penetration testing with a higher frequency to continually assess and strengthen their security measures.

To further enhance security practices, organizations can adopt agile pen testing or continuous pen testing. Unlike traditional pen testing, which occurs at specific intervals, agile pen testing integrates regular testing into the software development lifecycle (SDLC). This approach ensures that security assessments are conducted consistently throughout the development process, aligning with the release schedule of new features. By doing so, organizations can proactively address any vulnerabilities and mitigate risks to customers, without significantly impacting product release cycles.

When choosing a pen test provider, you'll want to consider several important factors to ensure your organization's highest level of cybersecurity.

Selecting the right pen test provider is crucial for your organization's security. It's about identifying vulnerabilities and having a partner who can help you remediate them effectively. To make an informed decision, here's what you should look for:

Expertise and Certifications: One of the key factors to consider is the expertise of the pen testers. Look for providers with a team of experts holding certifications such as CISSP (Certified Information Systems Security Professional), CSSLP (Certified Secure Software Life Cycle Professional), OSWE (Offensive Security Web Expert), OSCP (Offensive Security Certified Professional), CRTE (Certified Red Team Expert), CBBH (Certified Bug Bounty Hunter), CRTL (Certified Red Team Lead), and CARTP (Certified Azure Red Team Professional). These certifications demonstrate a high level of knowledge and competence in the field.

Comprehensive Testing Services: The cybersecurity landscape constantly evolves, and threats are becoming more sophisticated. To stay ahead, you need a provider with expertise and resources to test your systems comprehensively. Look for a pen test provider like Blue Goat Cyber that offers testing across various areas, including internal and external infrastructure, wireless networks, web applications, mobile applications, network builds, and configurations. This ensures a holistic evaluation of your organization's security posture.

Post-Test Care and Guidance: Identifying vulnerabilities is not enough; you need a partner who can help you address them effectively. Consider what happens after the testing phase. A reputable pen test provider should offer comprehensive post-test care, including actionable outputs, prioritized remediation guidance, and strategic security advice. This support is crucial for making long-term improvements to your cybersecurity posture.

Tangible Benefits: By choosing a pen test provider like Blue Goat Cyber, you ensure that you receive a comprehensive evaluation of your security posture. This extends to various areas, including internal and external infrastructure, wireless networks, web and mobile applications, network configurations, and more. The expertise and certifications of their team guarantee a thorough assessment.

Cloud penetration testing is a specialized and crucial process involving comprehensive security assessments on cloud and hybrid environments. It is crucial to address organizations' shared responsibility challenges while using cloud services. Identifying and addressing vulnerabilities ensures that critical assets are protected and not left exposed to potential threats.

Cloud penetration testing involves simulating real-world attacks to identify and exploit vulnerabilities within the cloud infrastructure, applications, or configurations. It goes beyond traditional security measures by specifically targeting cloud-specific risks and assessing the effectiveness of an organization's security controls in a cloud environment.

The importance of cloud penetration testing lies in its ability to uncover security weaknesses that might be overlooked during regular security audits. As organizations increasingly adopt cloud services, they share the responsibility of ensuring the security of their data and assets with the cloud service provider. This shared responsibility model often poses challenges regarding who is accountable for various security aspects.

Cloud penetration testing not only helps in understanding the level of security provided by the cloud service provider but also provides insights into potential weaknesses within an organization's configurations or applications. By proactively identifying these vulnerabilities, organizations can take necessary steps to mitigate risks and strengthen their security posture.

To ensure secure coding practices, development teams should undertake the following measures:

1. Promote Awareness: Development teams should be sensitized and educated about the importance of following secure coding practices. This can be achieved through training programs, workshops, and regular communication emphasizing the necessity of security in app development.

2. Mandatory Adoption: While creating organizational policies, it is crucial to mandate the use of secure coding practices. By making these practices a requirement, development teams will be encouraged to prioritize security throughout development.

3. Utilize Secure Libraries and Frameworks: Development teams should incorporate reliable and up-to-date secure libraries and frameworks during the app development process. These tools often have built-in security features and can help mitigate potential vulnerabilities.

4. Implement Secure Authentication: Robust and secure authentication mechanisms should be implemented to protect user accounts and sensitive information. This includes utilizing multi-factor authentication, strong password policies, and secure session management practices.

5. User Input Validation: Validate and sanitize user input thoroughly, both on the client-side and server-side, to prevent common vulnerabilities such as SQL injection and Cross-site Scripting (XSS). Implement appropriate input validation techniques to ensure user input does not lead to malicious actions or security breaches.

6. Robust Encryption Techniques: Data stored in the application's database should be encrypted using strong algorithms. Encryption helps prevent unauthorized access and protects sensitive data even during a breach.

7. Strict Access Controls: Implement stringent access controls to restrict unauthorized access to stored data. Employ user roles and permissions to ensure that only authorized individuals or entities can access sensitive information within the application.

8. Regular Testing and Security Audits: Regularly conduct security testing and audits to identify vulnerabilities and weaknesses in the codebase. This includes performing penetration testing, code reviews, and vulnerability assessments to address any potential security flaws proactively.

9. Stay Updated and Patch Vulnerabilities: Development teams should stay informed about the latest security practices, frameworks, and libraries. They should promptly address any reported security vulnerabilities by applying patches and updates to keep the application secure and up-to-date.

By adhering to these measures, development teams can significantly enhance the security of their codebase and protect the sensitive data within their applications.

Nikto is a powerful, freely available, open-source vulnerability scanning tool used to conduct comprehensive application tests. It employs over 6000 tests to identify potential security vulnerabilities and server misconfigurations. By thoroughly scanning the application, Nikto can pinpoint forgotten scripts, installed software, and any other weak points that may leave the application susceptible to attacks.

One of the key features of Nikto is its ability to perform more than 2000 HTTP GET requests. This serves the purpose of evaluating the effectiveness of Intrusion Detection Systems (IDS). This testing allows for a deeper understanding of whether the current security measures can detect and prevent unauthorized access or malicious activities.

It is important to note that Nikto operates primarily through a command line interface, offering advanced users the flexibility to customize and fine-tune the scanning process. However, as a command line tool, it lacks a graphical user interface (GUI), so it may require some technical expertise to navigate and interpret the scan results effectively.

Although Nikto itself is freely available, it should be noted that there may be associated costs with acquiring the data files containing information about specific exploits. These files are essential for identifying and examining potential vulnerabilities in the tested application.

Zed Attack Proxy, also known as ZAP, is an open-source vulnerability scanning application widely supported by a global community of volunteers. It serves as an intermediary between a web browser and an application, acting as a firewall. This allows ZAP to detect and analyze potential vulnerabilities. ZAP offers automated and manual scanning tools to identify vulnerabilities, whether used as a standalone application or a daemon process.

To perform a vulnerability scan, ZAP can operate in active or passive mode. In active mode, ZAP sends proof-of-concept (PoC) malicious requests to the target application and examines the responses to identify potential vulnerabilities. On the other hand, passive mode analyzes every response during the regular scanning process to uncover the same vulnerabilities as active scanning but without sending PoC requests.

For individuals new to vulnerability testing, ZAP is an excellent starting point. It provides extensive documentation and benefits from a supportive community to assist users in understanding how to utilize the tool effectively. With ZAP, users can gain deep insights into the security of their applications and identify potential weaknesses that attackers could exploit.

Burp Suite is a comprehensive application vulnerability scanning platform that is highly regarded by testers. Developed by the company that pioneered Automated OAST (out-of-band application security testing), Burp Suite replicates the actions of a skilled manual tester and excels at crawling even JavaScript-heavy applications.

One of the key strengths of Burp Suite is its ability to expose a wide range of existing application vulnerabilities. By extensively scanning an application, it efficiently identifies potential weaknesses, ensuring comprehensive coverage and reducing the likelihood of false positives.

In particular, Burp Suite safeguards against zero-day vulnerabilities, threats that exploit previously unknown software vulnerabilities. It achieves this by utilizing sophisticated location fingerprinting techniques during the crawling process. These techniques enable the platform to identify potential entry points for zero-day attacks, minimizing the risk of successful exploitation.

User input validation is crucial for web application security as it helps prevent common vulnerabilities. By validating user input, we can ensure that the data entered into the application meets the expected format and criteria. This is vital in mitigating risks associated with common vulnerabilities such as SQL injection, OS command injection, and cross-site scripting (XSS).

For instance, proper validation helps prevent SQL injection attacks where malicious actors attempt to manipulate the input to execute harmful SQL queries. By validating and sanitizing user input, we can ensure that special characters or SQL commands are not executed as intended, safeguarding the application's database from unauthorized access and data breaches.

Similarly, user input validation is effective in preventing OS command injection attacks. By carefully validating and sanitizing the user input, we can thwart attackers from injecting malicious commands into the system and executing arbitrary commands on the underlying operating system. This helps maintain the integrity and security of the application and the host environment.

Moreover, user input validation is crucial in preventing cross-site scripting attacks. By validating and sanitizing user input, we can prevent the injection of malicious scripts into web pages. This is a strong defense against unauthorized access, data theft, and other malicious activities arising from XSS attacks.

The investment for a comprehensive web application penetration test at Blue Goat Cyber starts at a minimum of $6000. This pricing reflects our commitment to delivering both automated and manual analysis, ensuring a thorough examination of your web application for vulnerabilities. Our process is not merely a one-time scan but a detailed assessment that includes:

  • Automated Analysis: Initial automated scans to quickly identify common vulnerabilities across the application.
  • Manual Analysis: Deep-dive manual testing conducted by our cybersecurity experts to uncover more complex security issues that automated tools can miss.
  • Retest Included: After vulnerabilities have been identified and you've had the opportunity to address them, we include a retest as part of our service. This ensures that the remediation efforts were effective and that your web application's security posture has been significantly enhanced.

We tailor our testing approach to the unique needs of your application, considering its architecture, technology stack, and the specific risks associated with your industry. This ensures a more accurate and effective testing process, providing you with valuable insights and actionable recommendations.

Choosing Blue Goat Cyber for your web application penetration testing means investing in a partnership dedicated to your long-term security. Our goal is to identify vulnerabilities and help you understand and mitigate them, ensuring your web application remains resilient against emerging cyber threats.

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