Web Application Penetration Testing Checklist [2025 Edition]
In today’s hyperconnected world, web applications are a major target for cybercriminals. Whether you're running a startup or managing an enterprise-grade platform, web application penetration testing is critical to identifying security flaws before attackers do. In this 2025 edition, we’ve compiled a complete web application penetration testing checklist—fully aligned with the latest OWASP Top 10, compliance requirements, and real-world threat vectors.
What is Web Application Penetration Testing?
Web application penetration testing is a simulated cyberattack performed on a web app to identify vulnerabilities that could be exploited by real attackers. Unlike automated scanners, manual web app pentesting mimics real-world hacking techniques to uncover logic flaws, broken authentication, insecure APIs, and more.
Why You Need a Web Application Pentest in 2025?
With rising threats like API abuse, MFA bypass, and business logic attacks, organizations can’t rely on automated tools alone. Conducting web application penetration testing in 2025 helps:
Prevent data breaches and reputational damage
Meet security compliance frameworks (e.g., SOC 2, HIPAA, ISO 27001)
Detect OWASP Top 10 vulnerabilities
Improve secure coding practices
Web Application Penetration Testing Checklist [2025]
Use this comprehensive checklist to ensure your web app security is thoroughly validated:
1) Reconnaissance & Information Gathering:
Start by collecting technical and contextual information about the target app.
Subdomain Enumeration – Identify all subdomains that might host web applications or admin portals using tools like Sublist3r, Amass, or Assetfinder.
DNS Zone Transfers – Check if zone transfer is misconfigured and leaking internal DNS records.
WHOIS Lookups – Discover domain ownership, registrar details, and email addresses to aid in social engineering or phishing scenarios.
Directory Brute Forcing – Use tools like Dirb, Ffuf, or Gobuster to find hidden folders, unlisted files, and backup endpoints.
JavaScript Analysis – Analyze JS files to uncover API endpoints, tokens, or developer comments containing sensitive data.
By mastering information gathering, you lay the groundwork for identifying misconfigured systems, hidden attack surfaces, and soft entry points.
2) Testing for Broken Authentication:
Broken authentication is a critical security risk that allows attackers to impersonate other users or gain unauthorized access to admin panels.
Test the following:
Default Credentials – Check if the app still accepts default usernames/passwords like
admin:adminoruser:password.Weak Password Policies – Analyze if the app allows short or easily guessable passwords without enforcement of complexity.
Password Reset Flaws – Attempt to abuse the password reset flow to change credentials without user verification.
Multi-Factor Authentication Bypass – Try bypassing MFA using cookie reuse, brute force, or misconfigured fallback mechanisms.
These tests simulate real-world attacker behavior, especially credential stuffing or session takeover attempts in insecure apps.
3) Testing for Authorization Issues (IDOR):
Insecure Direct Object Reference (IDOR) and broken access controls occur when users can access data or actions they're not authorized for.
Focus on:
Horizontal Privilege Escalation – Try accessing another user’s data by changing user IDs in URLs (e.g.,
/account?id=1002).Vertical Privilege Escalation – Test if a regular user can access admin functionality or protected resources.
Role-Based Access Control – Manipulate roles or tokens (like JWTs) to gain higher privileges.
OAuth/Token Abuse – Explore weaknesses in token generation, revocation, and scope restrictions.
These are high-impact flaws that can lead to data leakage, privilege abuse, and unauthorized actions.
4) Input Validation & Injection Attacks:
Improper handling of user input leads to critical injection vulnerabilities that can result in data theft, remote code execution, or full system compromise.
Test these attack types:
SQL Injection (SQLi) – Inject malicious SQL payloads to extract or manipulate database content.
Command Injection – Pass OS-level commands through vulnerable input fields to control the server.
Cross-site Scripting (XSS) – Insert scripts into input fields or parameters that execute in a user’s browser.
Server-Side Template Injection (SSTI) – Inject payloads into rendering engines like Jinja2 or Twig to gain backend access.
XML External Entity (XXE) – Exploit XML parsers to read internal files or cause denial-of-service.
Modern web app security testing requires both automated scanners and manual payload crafting to find hidden vectors.
5) Session Management Testing:
Session vulnerabilities can allow attackers to hijack authenticated sessions, impersonate users, or maintain unauthorized access.
Key session tests:
Insecure Cookies – Check for cookies without
HttpOnly,Secure, orSameSiteflags, making them vulnerable to XSS or MITM attacks.Session Timeout Issues – Ensure sessions expire after inactivity or logout and cannot be reused.
Session Fixation – Attempt to force a user to use a session ID known to the attacker.
Token Reuse or Theft – Test if old or stolen session tokens are still valid after logout.
These vulnerabilities often go unnoticed but are critical for web application security and user trust.
6) Security Testing for APIs & Endpoints:
Modern applications rely heavily on REST and GraphQL APIs, making them a top target for attackers.
Your checklist should include:
Sensitive Data Exposure – Test for personally identifiable information (PII) or credentials exposed in API responses.
Rate Limiting & Abuse – Check if the API allows brute-force attacks due to missing throttling or CAPTCHA.
Input Validation on Endpoints – Ensure all parameters are properly validated and sanitized.
GraphQL Introspection – Use introspection to reveal all schema types and operations if misconfigured.
Improper Authentication or CORS Config – Validate how APIs are protected across origins or devices.
Comprehensive API penetration testing is essential to securing modern single-page apps (SPAs) and mobile backends.
7) Business Logic Testing:
Business logic flaws are unique to each application and can't be detected by automated tools. This is where manual penetration testing shines.
Common flaws include:
Bypassing Payment Logic – Modify payment amounts or skip payment entirely.
Referral Code Abuse – Test repeated use of referral coupons for unintended benefits.
Order Tampering – Change prices, quantities, or delivery details in client-side requests.
Workflow Manipulation – Skip steps in a transaction (e.g., checkout before login).
These web application abuse scenarios are often missed in traditional testing but can cause serious financial and reputational damage.
8) Security Misconfigurations & Framework Testing:
Misconfigured environments are low-hanging fruit for attackers and often provide direct access to sensitive files or services.
Test for:
Open Directories & Exposed Files – Look for accessible backup files,
.git,.env, or database exports.HTTP Header Validation – Check for missing headers like
Content-Security-Policy (CSP),Strict-Transport-Security (HSTS), andX-Frame-Options.Outdated Frameworks or Libraries – Identify vulnerable versions of web frameworks (Laravel, React, Django) and frontend dependencies via
package.jsonorcomposer.lock.Default Error Pages – Check for stack traces or tech details that can aid an attacker.
Web server misconfigurations are easy to exploit, but also easy to fix—making them a high-priority for dev and DevOps teams.
9) Reporting & Documentation:
A well-documented penetration test report is just as important as the test itself. It helps developers and security teams understand the impact, risk level, and steps to remediate each finding.
A good report includes:
Executive Summary – Non-technical overview of test results and business impact
Technical Details – Step-by-step description of each vulnerability with payloads and screenshots
Risk Ratings – Based on CVSS or your organization’s scoring matrix
Remediation Guidance – Actionable steps developers can follow to fix each issue
Retesting Plan – Scope and timeline for verifying fixes
A strong web application security audit document builds credibility and supports compliance audits.
Conclusion:
Web application penetration testing in 2025 is no longer optional—it's a security essential. Use this checklist to perform in-depth testing across all attack surfaces, from login flows and APIs to session handling and logic flaws. If you’re looking for a professional penetration testing service provider, our team at Com-Sec offers manual web application security assessments, complete with compliance-ready reports and actionable remediation support.
