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Mastering Web App Penetration Testing: Your Ultimate Guide

We are halfway through the 2020s, yet data breaches still remain a problem. About 14% of them happen by exploiting vulnerabilities as the initial access point. Even worse, 98% of organisations reported doing business with a vendor who has suffered a data breach in the past two years.

With cybercrime on the rise, protecting your web applications and the data they store is non-negotiable. Web penetration testing is one way to do this. It’s a simulated ethical hacking that lets you identify vulnerabilities in your web app before malicious actors exploit them.

So, how do you use penetration testing to secure your apps? This guide will cover everything you need to know: core components to consider, steps to take, and tools to use. As a security-compliant software development company, GoodCore will provide you with the insights necessary for tackling vulnerabilities before they cost you a lot.

Understanding Website Penetration Testing

According to IBM’s Cost of a Data Breach Report 2023, penetration and application testing are among the most effective cost-saving measures in response to breaches. So, what exactly is web app penetration testing? Let’s get this straight.

What Is Website Penetration Testing?

Website penetration testing, or web application penetration testing, involves simulating a cyberattack against a web app to identify its vulnerabilities. The main goal of such testing is to find those weak spots before malicious actors can exploit them.

The vulnerabilities may include security misconfigurations, coding errors, flaws in application logic, and beyond. Checking for them regularly helps developers and security professionals decide whether corrective actions and additional security measures are necessary.

Importance of Web Penetration Testing

Web application pen testing helps you check every part of your app: its database, frontend, and backend. Here are several reasons why this is important:

  • Data security. Web application pentesting is a way of protecting sensitive data from unauthorised access, modification, or deletion.
  • Reduced risk of breaches. Penetration testing identifies and addresses loopholes in your web app so that it can withstand cyberattacks.
  • Regulatory compliance. Web app pen testing helps you comply with industry regulations and security standards, including PCI DSS, HIPAA, etc.
  • Infrastructure assessment. Penetration testing lets you evaluate the strength of public-facing infrastructure components like firewalls and DNS servers.

Core Components of Effective Penetration Testing

An effective web application pen test depends on two major components: using different testing types and strictly following penetration testing phases. Let’s discuss these in greater detail.

Types of Penetration Tests

There are two main types of penetration tests:

Penetration Testing TypeAttacker’s PerspectiveTarget
Internal penetration testingSimulates an attack from inside the organisation’s network. Mimics an insider whose credentials were compromised or an attacker who has gained limited access.Targets the web app hosted on the organisation’s intranet.
External penetration testingSimulates an attack from the internet as if an external attacker was trying to gain unauthorized access to the system.Targets the organisation’s publicly accessible assets: the web app itself, the company website, and DNS.

Phases of Penetration Testing

Web app pentesting follows four key phases: reconnaissance, mapping, vulnerability assessment, and exploitation. Let’s get each of them straight:

  1. Reconnaissance. In this initial phase, the tester gathers information about the target system, including its purpose, network topology, technology stack, user accounts, and other relevant details. This involves researching OSINT and other publicly available sources.
  2. Mapping. Once all the relevant data is collected, the tester continues exploring the target system. They may use various tools (Nmap, Shodan, DNSDumpster) to identify open ports and network traffic to better understand the system’s architecture and potential attack surfaces.
  3. Vulnerability assessment. The next phase is where the tester uses the discovered data to identify specific weaknesses within the system. Then, they decide on how to exploit the vulnerabilities.
  4. Exploitation. In this phase, the tester attempts to exploit the identified vulnerabilities to access the system or its data, typically by using tools like Metasploit. This stage lets the tester evaluate the severity of the system weaknesses and the potential impact of a real-world attack.

How to Conduct Website Penetration Testing Step-by-Step

The main stages of website penetration testing

Now that you know the web app penetration meaning and components, let’s explore the practical steps involved. Here’s how our experts at GoodCore prepare and conduct web application security testing:

Setting Up Your Testing Environment

Before actually hacking the web app, you should prepare a solid foundation. Here’s what you need to get started:

  1. Define the scope. Set the boundaries of your penetration test. Decide on the specific web app aspects you’ll be checking and the testing methods you’ll use. Outline the desired outcomes and goals of the test (e.g., ensure compliance or evaluate overall app protection).
  2. Gather information. The more you know about your target application, the more effective your testing will be. Go through the reconnaissance phase and collect info about the tech stack, app features, network and domain names, and any known vulnerabilities.
  3. Select necessary tools. Equip yourself with the tools necessary for the job. They may include vulnerability scanners, web app security testing software, or specialised penetration testing software.

Performing the Test

With the environment prepared, move on to web app penetration testing. Make sure to follow these steps:

  1. Run automated scans. Use automated tools to scan the web app for weaknesses and misconfigurations. Run different scans, including code analysis and network vulnerability testing.
  2. Perform manual testing. Once you get your scan results, review the findings to remove false positives — i.e., confirm the authenticity of the found vulnerabilities. Then, keep testing your app to identify more complex issues like payment gateway or business logic errors.
  3. Exploit the vulnerabilities. Try to exploit the identified weaknesses to gain unauthorised access, steal data, intercept traffic, or perform other malicious actions. Document each step, including how exactly the vulnerability was exploited.
  4. Develop a proof-of-concept. For critical vulnerabilities, create a proof-of-concept that demonstrates the potential impact of a successful exploit. This way, you’ll be able to effectively communicate the vulnerability’s severity to stakeholders.
  5. Analyse conducted tests. Post-exploitation, prepare a comprehensive report with web security testing results. Cover the activities performed, vulnerabilities identified, exploitation attempts, and recommendations for remediation and encryption measures.

Feeling overwhelmed? Let our experienced team handle web app penetration testing for you.

Essential Tools and Techniques for Penetration Testing

You need various website penetration testing tools to handle the tests successfully. Let’s see what exactly you can leverage.

Popular Tools Used in Penetration Testing

To test your web application, it’s necessary to install apps and tools for penetration testing. Their selection is extensive:

  • ZAP. It’s an open-source web application security scanner suitable for beginners and experienced testers alike. ZAP provides a user-friendly interface for manual testing and offers automated scanning as well.
  • Burp Suite. It’s a comprehensive suite of tools for web application vulnerability assessment and penetration testing. It lets you identify vulnerabilities, automate attack sequences, scan APIs and SPAs, and minimise false positives.
  • Metasploit. It’s a web application penetration testing framework that lets you develop and execute exploit code against a target system. It offers an extensive database of exploits and payloads, tools for manual exploitation, phishing awareness management, and other features.
  • Nmap. It’s a network mapping tool that allows you to discover hosts and services on a computer network, thus providing a map of the network’s structure. It identifies open ports, operating systems, ping sweeps, and more.
  • Shodan. It’s a search engine for Internet-connected devices, which lets you find information about devices (webcams, routers, servers) that are publicly accessible. It helps you get insights into the exposed services and their potential weaknesses.
  • DNSDumpster. It’s a tool used for DNS reconnaissance. You can get an overview of subdomains, mail servers, name servers, and other relevant DNS records.

Manual vs. Automated Testing

Manual and automated testing are both necessary for a comprehensive check of your web app. Here’s a breakdown of their strengths and weaknesses:

Testing MethodStrengthsWeaknesses
ManualIn-depth analysis, including the app’s business logicAbility to identify unconventional vulnerabilitiesCustomised testing strategies based on findingsTime-consuming and labour-intensive Repetitive tasks may be subject to human error
AutomatedEfficient for scanning large codebases and identifying common vulnerabilitiesProvides consistent and repeatable resultsSaves time and effortMay miss complex vulnerabilities or those requiring specific configurations

Advanced Penetration Testing Concepts and Education

As technologies are getting more advanced, so are the methods attackers use to exploit vulnerabilities. Thus, after pen testing a website, make sure your security measures get more robust as well.

Advanced Techniques and New Threats

According to IBM, the average data breach cost in 2023 was $4.45 million, a 15% increase over three years. So, investing in security now can save you millions in the future. For example, organisations that extensively use security AI and automation save $1.76 million compared to those that don’t.

Data stored in the cloud is particularly at risk, with 82% of breaches involving cloud-based data. Consequently, penetration testers need to be well-versed in cloud-specific vulnerabilities and testing methodologies.

Security testing methods

Another emerging trend is integrating security throughout the entire development lifecycle. In this case, DevSecOps is gaining specific prominence. On top of that, IBM identified it as one of the best cost-saving factors.

Continuous Learning and Certification

The evolving website penetration testing field requires continuous learning and professional development. Here are a few ways you can keep up with the trends:

  • Certification programs. Earn a recognised web application penetration testing certification to validate your skills and knowledge. The best options include OSCP (Offensive Security Certified Professional), CEH (Certified Ethical Hacker), and GWAPT (GIAC Web Application Penetration Tester).
  • Online resources. Follow the latest news and trends online through video courses, penetration testing labs, and free tutorials.
  • Industry conferences and training. Participate in dedicated events and specialised training programs to learn about the latest developments in penetration testing and emerging threats.

How GoodCore Can Help with Web App Penetration Testing

For almost 20 years, GoodCore has been delivering unparalleled web app development services. The applications we build are secure, compliant, and always tailored to our client’s requirements. Here’s how we make that possible:

  •  Highly skilled web app developers using the latest tech stack.
  • Efficient project management to deliver your app on time and within budget.
  • Flexible team to meet any of your evolving demands.
  • Keeping you updated throughout the process.

Offering end-to-end web application development, we handle thorough testing along the way. In particular, we conduct security checks, with penetration testing as part of them. Our web application penetration testing checklist includes:

  • Defining the testing scope. We identify which parts of your web app will be tested, along with your goals and desired outcomes.
  • Collecting the info on your app. We study your app’s tech stack, features, and architecture.
  • Assessing the vulnerabilities. We identify security weaknesses in your web app through automated and manual testing.
  • Exploiting the vulnerabilities. We try to exploit the identified vulnerabilities in a controlled environment to understand their potential impact.
  • Suggesting remediation scenarios. Based on the testing results, we provide recommendations on how to fix the discovered vulnerabilities.
Phases of website penetration testing

Since cybersecurity is developing rapidly, GoodCore aims to stay ahead of the curve. Recently, our team was evaluated and certified by Cyber Essentials, a UK-based vendor supported by the National Cyber Security Centre (NCSC). Therefore, we are knowledgeable about the most effective ICT defences against common cyber threats.

A BriefingSource briefing management platform secured by web penetration testing

One recent example of our work is BriefingSource, a briefing management platform. The client set high standards for data security and privacy, requiring their product to comply with GDPR and SOC2/Type2 regulations. To meet these requirements, we implemented authorised access and single sign-on mechanisms, identity management, data encryption, regular security audits, and comprehensive privacy policies. As part of this project, we also handle quarterly penetration tests.

Learn more about website penetration testing services in our detailed case studies.


In the face of rising data breaches, web penetration testing has become an invaluable security measure. By following our guide on how to do penetration testing for a website or app and combining manual and automated testing techniques, you’ll be able to improve your web application’s security posture.

In case you want to secure help from professionals, you can count on GoodCore’s many-year experience to achieve the utmost security of your software. Just drop us a line to discuss your specific needs.


What should I do after a web application penetration test?

First, you create a report with all the identified vulnerabilities, ranking them by their severity, impact, and ease of exploitation. Then, you need to develop a remediation plan — the steps you should take to fix the issues. After remediation, conduct application pen testing once again to ensure all vulnerabilities have been successfully tackled.

How often should I conduct web application penetration testing?

Generally, it’s best to handle web app pen testing at least once or twice a year. Besides just regular checks, perform a test whenever there are significant changes to the application or after a security incident or breach.

Can a pen test damage my web application?

Website penetration testing is generally safe. Yet, there’s a small risk of damage, especially if the test involves aggressive scanning or exploitation. To avoid any risks, make sure that the website penetration testing service is performed by professionals — best if they’re certified.

What are some limitations of web application penetration testing?

While penetration testing of websites or web apps is increasingly helpful, it has certain limitations. They are:

  • Scope constraints. Penetration tests are limited by the pre-defined scope, which may not cover all potential attack vectors.
  • False positives. Automated testing tools may suggest false positives (non-issues marked as vulnerabilities), so you must check everything manually.
  • Human factor. The test’s effectiveness and accuracy depend on the skills of the testers, which may vary.

What are some alternatives to web application penetration testing?

If, for some reason, a penetration test of a web application isn’t suitable for you, you can opt for several alternatives. Those include automated vulnerability scanning, manual or automated code reviews, security audits, automated breach simulations, and using CI/CD security tools.

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Asad Ul Islam

The author Asad Ul Islam

Asad Islam is the Vice President of Engineering at GoodCore Software, where he brings an impressive 19-year track record in the IT industry to his leadership role. An expert in delivering high-quality software solutions on time and within budget, Asad thrives on technical complexity and has deep skills in architecting complex software spanning across a wide spectrum of tech stacks. His expertise spans all facets of the project lifecycle for software development and IT, leading development teams to achieve ambitious targets, making him a pivotal figure in driving GoodCore’s technical strategy and innovation.

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