Modern software handles important business processes, customer information, payments, integrations, and access to other systems. That makes application security an important part of software development.
Automated security tools can identify many potential vulnerabilities, but they cannot always show whether a weakness can actually be exploited or how different weaknesses could work together.
This is where software penetration testing adds value.
Software penetration testing is an authorised security assessment in which specialists test an application for vulnerabilities and safely investigate whether those weaknesses can be exploited.
Unlike penetration testing that focuses on networks, infrastructure, or physical security, software penetration testing concentrates on the application itself, including web applications, mobile apps, APIs, authentication, access control, data handling, and application logic.
This guide explains how software penetration testing works, the vulnerabilities it can identify, the different types of application penetration testing, where it fits in the software development lifecycle, and what businesses should consider when choosing a testing partner.
What Is Software Penetration Testing?
Software penetration testing, sometimes called software pen testing or application penetration testing, is a security assessment designed to identify exploitable vulnerabilities in software applications.
A tester examines the application from a security perspective and attempts to validate weaknesses under controlled and authorised conditions.
The important distinction is between identifying a possible vulnerability and understanding whether it can actually be exploited.
For example, an automated security tool may identify potentially unsafe input handling. A penetration tester can investigate whether that weakness could allow unauthorised access to information, affect application behaviour, or compromise another part of the system.
This combination of tools, manual investigation, and human judgment is what separates penetration testing from automated vulnerability scanning alone.
Why Software Applications Need Penetration Testing
Applications change continuously.
New features are added, APIs are introduced, dependencies are updated, authentication flows change, and applications connect to more external services.
Each change can affect the application’s security.
The original content references Veracode’s State of Software Security research, which highlights the prevalence of security flaws in applications and the growing importance of vulnerabilities in third-party and open-source components.
Software penetration testing helps businesses investigate these risks from the perspective of someone actively looking for a way to exploit them.
It can help a business:
- Identify exploitable application vulnerabilities
- Understand the potential impact of security weaknesses
- Find problems in authentication and access control
- Assess APIs and application integrations
- Identify business-logic weaknesses that automated tools may miss
- Prioritise remediation based on actual risk
- Validate application security before important releases
The purpose is not to guarantee that an application can never be attacked.
It is to give the business and development team a clearer understanding of where meaningful application security risks exist and what should be addressed.
Common Software Vulnerabilities Penetration Testing Can Find
Software penetration testing looks for weaknesses across the application, including areas covered by recognised resources such as the OWASP Top 10 and MITRE CWE.
Common examples include:
| Vulnerability | What It Means |
| Injection Flaws | Untrusted input affects a database, command, or application behaviour in ways that were not intended |
| Cross-Site Scripting (XSS) | Malicious scripts can be introduced into content viewed by other users |
| Broken Access Control | Users can access information or actions beyond what their permissions should allow |
| Authentication Weaknesses | Problems with login, credentials, or session management create opportunities for unauthorised access |
| Insecure APIs | APIs expose information or functionality without appropriate authentication, authorisation, or input controls |
| Vulnerable Dependencies | Third-party libraries, frameworks, or components contain known security vulnerabilities |
| Security Misconfiguration | Application or service settings unintentionally expose functionality, data, or administrative capabilities |
Not every vulnerability creates the same level of risk.
One of the important roles of a penetration test is to investigate the potential impact of a finding and help the development team understand what should be prioritised.
A tester may also find that several individually smaller weaknesses can be combined to create a more significant security issue.
Types of Software Penetration Testing
The right type of application penetration testing depends on the software being assessed.
A web application, mobile application, and API each have different attack surfaces and security considerations.
| Type | What It Tests | Typical Areas of Focus |
| Web Application Penetration Testing | Websites, portals, SaaS products, and browser-based applications | Authentication, access control, inputs, sessions, business logic, and data handling |
| Mobile Application Penetration Testing | iOS and Android applications | Local data storage, authentication, device interaction, APIs, and communication with backend systems |
| API Penetration Testing | APIs used by web, mobile, and integrated systems | Authentication, authorisation, input handling, data exposure, and endpoint behaviour |
| Cloud-Native Application Testing | Applications using cloud services, microservices, or containers | Application configuration, permissions, service interaction, and exposed resources |
| Desktop Application Testing | Installed desktop or thick-client applications | Local storage, application permissions, update mechanisms, and communication with backend systems |
For many businesses, web application penetration testing and API penetration testing are natural priorities because these systems may be directly accessible from the internet and handle important business or customer data.
The scope should ultimately reflect where the application’s most important security risks are.
The Software Penetration Testing Process
A professional software penetration test should follow a structured methodology rather than relying on ad hoc testing.
The exact activities depend on the application and agreed scope, but a typical process includes:
| Stage | What Happens |
| 1. Scoping | Define the applications, environments, functionality, testing boundaries, timing, and permitted techniques |
| 2. Application Mapping | Understand the application’s pages, inputs, APIs, authentication flows, roles, integrations, and technologies |
| 3. Security Testing | Test the application systematically for potential security weaknesses |
| 4. Exploitation & Validation | Safely investigate selected findings to understand whether they can be exploited and what impact they could create |
| 5. Reporting & Remediation | Document findings, severity, evidence, potential impact, and recommended remediation |
| 6. Retesting | Test identified vulnerabilities again after remediation to confirm that they have been addressed |
Scoping is particularly important because penetration testing involves deliberately attempting actions that normal users should not be able to perform.
The testing boundaries and authorisation should therefore be clear before the engagement begins.
Reporting is equally important. A useful penetration test should give developers enough information to understand and address the vulnerability rather than simply providing a list of security findings.
Where Penetration Testing Fits in the SDLC
Penetration testing in the SDLC works best as part of a broader application security approach rather than as a single activity immediately before launch.
Security can be considered at several stages of software development.
| SDLC Stage | Security Activity |
| Planning & Design | Identify security requirements, sensitive data, access requirements, and important risks |
| Development | Apply secure coding practices and review security-sensitive functionality |
| Build & Integration | Use automated security tools to identify known issues and vulnerable dependencies |
| Pre-Release | Perform deeper application security testing and penetration testing where appropriate |
| Post-Release | Monitor vulnerabilities, maintain dependencies, and test again after significant changes |
| Ongoing Maintenance | Combine regular scanning with periodic manual penetration testing |
This approach is often associated with shift-left security or DevSecOps.
The idea is straightforward: identify security issues as early as practical while still using deeper testing at important points in the development lifecycle.
Automated tools can provide frequent feedback during development. Manual penetration testing can then investigate application logic, attack paths, and vulnerabilities that require human reasoning.
For fast-changing applications, this combination can provide more useful security coverage than relying on a single penetration test at the end of development.
How AI Changes Application Security Testing
AI-assisted development can help teams produce and iterate on software more quickly.
However, faster development does not remove the need for security review and testing.
Code that functions correctly can still contain security weaknesses, regardless of whether it was written manually or with AI assistance.
As development becomes faster, security practices need to keep pace. Automated security testing can help provide frequent feedback, while manual penetration testing remains useful for investigating vulnerabilities that depend on application context, business logic, or combinations of weaknesses.
The principle remains the same: development speed should be supported by appropriate review and testing.
Software Penetration Testing vs. Automated Security Scanning
Automated security scanning and manual penetration testing are both useful, but they solve different problems.
Tools such as SAST, DAST, and SCA can identify known patterns, vulnerable dependencies, and potential security issues throughout development.
Penetration testing adds human investigation and validation.
| Area | Automated Security Scanning | Software Penetration Testing |
| Approach | Automated tools analyse code, dependencies, or running applications | Security specialists manually investigate the application, supported by tools |
| Frequency | Can run frequently or as part of the development pipeline | Usually performed at selected points or periodically |
| Known Vulnerabilities | Effective at identifying many known patterns and issues | Can validate and investigate identified weaknesses |
| Business Logic | Limited understanding of application context | Human testers can investigate how application logic could be abused |
| False Positives | Findings may require further validation | Findings are investigated and validated during testing |
| Best Use | Frequent security feedback during development | Deeper assessment of exploitable application risk |
The two approaches are complementary.
Automated scanning can provide broad and frequent coverage, while manual penetration testing provides deeper investigation where human judgment and application context matter.
Software Penetration Testing and Compliance
Penetration testing can also help businesses meet security and compliance requirements.
Depending on your industry, customers, and the type of data your software handles, you may need to show that your applications are regularly tested for security risks.
Common frameworks and regulations include:
- PCI DSS for businesses that handle payment card data
- ISO 27001 for information security management
- SOC 2 for organisations that need to demonstrate how they protect customer data
- GDPR for protecting personal data
The exact requirements vary. Some frameworks may require specific security testing, while others require businesses to demonstrate that security risks are being properly identified and managed.
A penetration test does not automatically make your business compliant. However, it can provide useful evidence that your applications are being actively tested and that identified security risks are being addressed.
A mature software security testing approach may use both.
How Often Should Software Be Pen Tested?
There is no single penetration testing schedule that applies to every application.
The right frequency depends on factors such as:
- How often the application changes
- The sensitivity of the data involved
- Whether the application is internet-facing
- The importance of the application to business operations
- Customer or contractual requirements
- Applicable compliance requirements
Businesses commonly consider software penetration testing:
- Before launching an important new application
- Before or after a significant release
- After major changes to authentication, permissions, APIs, or architecture
- After significant infrastructure changes that affect the application
- Periodically for important or high-risk applications
- When required by a customer, contract, or compliance programme
The original brief suggests annual testing as a common baseline for important software, with additional testing after major changes.
Between manual penetration tests, automated scanning can provide more frequent security feedback.
How to Choose a Software Penetration Testing Partner
Choosing a software penetration testing partner involves more than comparing prices.
The quality of the engagement depends heavily on the people performing the assessment, their understanding of application security, and the usefulness of the final report.
Look for Manual Testing and Expert Analysis
Automated tools should support the process, not replace specialist investigation.
Ask how the provider combines automated tools with manual testing and how findings are validated.
Manual testing is particularly important for business logic, authorisation, complex workflows, and combinations of vulnerabilities that automated tools may not understand.
Look for Application Experience
Software penetration testing is different from general network security testing.
The testers should understand how modern software is designed and built, including web applications, APIs, authentication, permissions, integrations, and relevant frameworks.
This also helps when explaining remediation to developers.
Review the Reporting Approach
A penetration testing report should clearly explain:
- What was found
- How serious the vulnerability is
- How it was validated
- What the potential impact is
- What the development team should do next
Ask whether the provider can show an example of its reporting structure before the engagement begins.
Ask About Retesting
Fixing the vulnerability is ultimately the important part.
Check whether the provider offers retesting after remediation so the development team can confirm that the identified weakness has been addressed correctly.
What Does Software Penetration Testing Cost?
Software penetration testing cost depends on the size, complexity, and scope of the application.
A small application with a limited number of user roles and functions requires a different level of effort from a complex platform with multiple APIs, integrations, permissions, and user types.
| Cost Factor | How It Affects Testing |
| Application Size | More functionality and workflows generally require more testing time |
| Application Complexity | Complex roles, permissions, integrations, and business logic increase testing effort |
| Number of Applications or APIs | Testing multiple systems increases the scope |
| Testing Depth | Broader or deeper assessments require more specialist time |
| Environment | Web, mobile, API, desktop, and cloud-native applications require different testing approaches |
| Retesting | Additional testing may be required after remediation |
A focused test of one web application, mobile application, or API can be a practical starting point when the risk area is clearly defined.
For businesses with several applications or rapidly changing software, testing may also be planned as a recurring activity rather than a single engagement.
The right starting point is to define what needs to be tested and why. From there, the testing partner can scope the effort more accurately.
How Manao Software Approaches Software Penetration Testing
Manao Software has more than 19 years of experience building software for businesses in Thailand and internationally.
Our web application penetration testing services focus on identifying meaningful application security risks and giving development teams practical information they can use to address them.
Our approach includes:
- Structured testing: The engagement starts with a clear scope and follows recognised application security practices.
- Manual investigation: Automated tools support the process, while human testing is used to investigate application logic and validate vulnerabilities.
- Application understanding: Our wider software development experience helps us understand how applications, APIs, integrations, and infrastructure work together.
- Clear reporting: Findings are prioritised and explained for both technical teams and business stakeholders.
- Practical remediation: Development teams receive guidance they can use when addressing identified vulnerabilities.
- Retesting: Identified issues can be tested again after remediation.
Manao is also an ISTQB Gold Partner, reflecting our wider commitment to software quality and testing practices. For software penetration testing specifically, our focus is on appropriate security methodology, application knowledge, manual investigation, and actionable reporting.
Security testing works best when it connects back to how software is developed and maintained. The objective is not simply to produce a security report. It is to identify meaningful risks and give the team the information needed to address them.
Straight talk. Solid delivery.
Planning a Software Penetration Test?
Software penetration testing can provide a clearer view of how an application could be exposed and which vulnerabilities should be addressed first.
The right engagement starts by defining the application, its most important functionality, the data it handles, and the security risks that matter most.
Manao Software provides web application penetration testing services for businesses that want to understand their application security risks and receive practical guidance on what to address.
Talk to Manao Software about your software penetration testing requirements.
