By 2025, the first point of entry to business, customer engagement, and sensitive data will be via applications. However, each of the lines of code, API connections, and misconfigured permissions may become part of the threat vector. This is a pity when we consider that many organizations place emphasis on defending the network levels, yet the application-level weaknesses are unnoticed.

Security gap assessment fills such a blind spot. It determines gaps between your existing application security positioning and the best practices or compliance guidelines and systems that you want to adhere to.

This guide will also teach you how to complete a comprehensive, value-based application security gap analysis step-by-step. We will deconstruct which analysis to do, who the players are, available tools, and action to be taken after conducting the analysis.

What Is an Application Security Gap Assessment?

An application security gap assessment is a systematic review that estimates the conformity of your existing app security practices against methodologies such as OWASP ASVS, NIST, or ISO 27001.

It is aimed at highlighting the vulnerabilities, weak points, and any gaps in the application development life cycle (SDLC), from design to deployment.

Key Objectives:

Identify exploitable vulnerabilities
Evaluate development and DevSecOps practices
Uncover misconfigurations, over-privileged access, or insecure integrations
Align application security with regulatory or internal benchmarks

Step 1: Define Scope and Objectives

Start by describing what you would like to evaluate:

Is it a web application, mobile application or cloud-native application, or a legacy application?
Are you evaluating only the code, or also the infrastructure, APIs, and access controls?
Do you want to align with OWASP Top 10, NIST, PCI DSS, or internal policies?

Scope is defined by: Detection of sensitive workflows (ex, login, payment, upload data), Deciding about what teams and environments to involve

Endpoints, modules, and APIs listing
Detection of sensitive work flows (ex: login, payment, upload data)
Deciding about what teams and environments to involve

Tip: Clear scope avoids wasted effort and ensures focused results.

Step 2: Stack Inventory of the Applications

Create an inventory of all that makes the app work:

Programming languages and frameworks used
Backend services and databases
Authentication and authorization systems
Third-party components, libraries, or APIs

How can you protect what you do not know is there? Most risks of the applications lie in the unmonitored information, old libraries, or hidden APIs.

Step 3: Review Existing Security Controls

Assess the level of security solutions that exist:

Secure coding standards and checklists
SAST (Static Application Security Testing) tools
DAST (Dynamic Application Security Testing) tools
Dependency scanning and SBOM tools
Web Application Firewalls (WAFs)
Authentication (MFA, OAuth, SSO)

Check if these controls:

Are consistently applied across teams
Generate actionable reports
Have alerting, monitoring, and incident response workflows

Note: Several controls are in place, but incorrectly configured or outdated—this is a major gap.

Step 4: Threat Modeling

Before testing begins, build a threat model to:

Map data flows and attack surfaces
Identify trust boundaries and privilege escalation paths
Prioritize components by risk

Systematically evaluate threat using models ( e.g., STRIDE or DREAD ).

This will aid in steering your penetration tests as well as the actions carried out during secure code reviews.

Step 5: Run Vulnerability Scanning and Manual Testing

Automated Scanning:

Run SAST for code issues (e.g. input validation, hardcoded secrets)
Run DAST on live environments for misconfigurations and business logic flaws
Scan third-party packages for known CVEs

Manual Testing:

Focus on complex attack paths (e.g. chaining broken access control + insecure direct object references)
Check rate limitations, security of sessions, and error handling
Check third-party packages against known CVEs

Combine tools like:

OWASP ZAP, Burp Suite
SonarQube, Snyk, GitHub Advanced Security

Step 6: Review DevSecOps and SDLC Integration

A security gap is not always a technical failure- it may be a process failure.

Review:

Do developers have secure coding? Is a security check involved in every build? Does CI/CD have automated testing?

Do developers have secure coding?
Is a security check involved in every build
Does CI/CD have automated testing

Interview developers, testers, and DevOps to uncover:

Where security is skipped under deadline pressure
Where manual steps create inconsistency or exposure

Step 7: Assess Governance, Policy and Awareness

Even the best tools fail without good governance. Check if:

You have written application security policies
Developers know the policies and follow them
Risk ratings and severity levels are defined consistently
Incident response plans cover app-specific threats

Look for signs of compliance drift, especially in fast-moving teams or M&A environments.

Step 8: Prioritize Gaps and Report Findings

It affects either users or data, or business continuity

Risk severity (Critical, High, Medium, Low)
Likelihood of exploitation
Impact on users, data, or business continuity
Ease of remediation

Deliverables:

Executive summary with top risks and recommendations
Technical breakdown with evidence, screenshots, and CVE references
Compliance mapping (e.g., PCI DSS Req 6.6, OWASP A3)

Your report must not detail problems; it must give direction.

Step 9: Build a Remediation Plan

Develop a remediation plan in which:

Gives out ownership of every problem
Incorporates schedules as well as its policies on risk acceptance
Suggests quick wins and long-term hardening steps

After fixing, apply a re-test in order to make sure that it is closed.

Final Thoughts

Application security gap analysis moves beyond scanners. It integrates code, infrastructure, policy and process audit to provide a holistic picture of your app risk.

This is not a choice in the modern environment of quick releases, third-party dependencies, and the increasing threat to the supply chain.

How to Perform a Comprehensive Application Security Gap Assessment