Application Security: Example, Workflow & Best Practices

Network and infrastructure security still matter, but they’re no longer enough on their own. These days, attackers aren’t wasting time trying to break through firewalls—they’re going straight for your code, and they’re getting in. Nearly half of all data breaches now happen at the application layer, making application security a critical part of your process from day one.

What is application security?

Application security (AppSec) is the set of tools and practices used to protect software from threats at both the code and runtime levels. Unlike network or infrastructure security, which builds walls around your systems, AppSec puts safeguards directly into the application itself—at the source code and compiled code levels.

Think of it this way: network security keeps malicious traffic from reaching your servers, but it doesn’t touch your code. AppSec, on the other hand, makes sure that even if that traffic gets through, it can’t do any damage. It might validate and sanitize inputs, protect sensitive data in memory, or block suspicious behavior at runtime. The goal is to make your application resilient, even when it’s exposed to direct attack.

Why it matters

Attackers today are getting smarter. They know most organizations focus on perimeter security, and they’re exploiting the gaps inside the app itself. That’s why application-layer attacks have become so common and so dangerous.

These attacks often lead directly to the most valuable assets: source code, customer data, API keys, and even encryption credentials. For example, in a reverse engineering attack, hackers might extract encryption keys from a banking app and use them to steal account information or authorize fraudulent transactions.

Some of the most common AppSec threats include:

• SQL injection (SQLi)
• Cross-site scripting (XSS)
• Cross-site request forgery (CSRF)
• API abuse
• Tampering and IP theft
  

As cyberattacks grow more sophisticated and as apps become central to everything from banking to healthcare, application security is no longer optional. It’s critical.

Building application security into the software development lifecycle

Application security only works if it’s built into every stage of the software development lifecycle (SDLC), not just added at the end. The workflow below shows how to make security a natural part of your process, from planning and design to deployment and beyond.

Risk assessment and planning phase (week 1-2)

Security threats vary widely depending on the industry and application. A financial app might be targeted for sensitive banking information, while a healthcare platform could face risks related to medical data phishing. This is why it’s so important to start with a proper risk assessment.

Early in the SDLC, your team should align security goals with business requirements and compliance standards. At a minimum, this phase should include:

• Threat modeling sessions: Bring together your security, development, and product teams to map out potential attack vectors specific to your app.
  
• Security requirements definition: Set clear security acceptance criteria for each feature. For example, “The authentication module must implement certificate pinning to prevent man-in-the-middle attacks.”
  
• Asset identification: Identify and document your app’s most sensitive data and components so they can be prioritized for protection.

Design phase (week 2-3)

This is where your security plans start to take shape. In the design phase, you translate requirements into architecture, and every design decision is a chance to strengthen your app’s defenses.

Key steps at this stage include:

• Security architecture review: Look closely at how data flows through your system. For example, make sure authentication services never send unencrypted credentials, even internally between components.
  
• Use secure design patterns: Follow proven practices like the principle of least privilege. Your app should only request the permissions it actually needs, and your settings module shouldn’t have access to location services unless it truly requires it.
  
• Define protection strategies: Decide how you’ll protect key assets. That might mean string encryption for hardcoded credentials, obfuscation for proprietary logic, or anti-debugging for authentication functionality.

Development phase (week 3-6)

Things start to get real during the development phase: It’s where all the security measures you planned earlier become actual code. You need to be especially careful here, as vulnerabilities can easily be introduced through unsafe coding practices, third-party libraries, or implementation mistakes. The good news is that this is also the most cost-effective stage to catch and fix security issues.

To stay secure during development, focus on:

• Secure coding practices: Follow language-specific best practices. For example, in Java, use PreparedStatements instead of string concatenation to avoid SQL injection.
  
• Security-focused code reviews: Conduct targeted reviews of high-risk components like authentication workflows. Your peer review checklist should specifically include verification of secure credential storage and proper session management implementation.
  
• Frequent SAST scans: Use static application security testing (SAST) tools as part of your daily builds, not just at the end of development. Tools like Kiuwan can flag insecure cryptographic implementations early, before they become real risks in production.

Build and testing phase (week 6-8)

This phase is your last opportunity to identify security issues before app deployment. It’s also your last chance to simulate whether the security controls you formulated in the earlier phases work as intended under realistic conditions. While it can look different from app to app, here’s what this phase should include:

• Build-time hardening: Apply code obfuscation, string encryption, and debug protection during the build process. Your CI/CD pipeline should automate these steps, especially for sensitive code sections identified during the planning phase.
  
• Dynamic application security testing (DAST): Run dynamic tests to simulate real-world attacks on your running application. These tests help you evaluate the effectiveness of your security measures and uncover potential vulnerabilities. (The exact tests will vary based on your application—for instance, a financial app should be tested for authentication bypass and transaction manipulation.)
  
• Penetration testing: Bring in security experts to attempt reverse engineering of protected components. Your assessment should include clear success criteria—for example, any attempt to bypass authentication through binary modification should be detected and blocked.

Deployment phase (week 8)

The deployment phase is when your application security measures transition from a controlled development environment to a hostile production world. It’s critical to verify that your security measures hold up under production conditions.

Key steps include:

• Secure deployment verification: Make sure all security controls still work as expected in the production environment. Confirm that runtime application self-protection (RASP) mechanisms function properly under live configurations and workloads.
  
• Certificate and key rotation: Put your key management plan into action. This includes regularly rotating API keys, encryption keys, and certificates to reduce long-term exposure.
  
• Security telemetry activation: Enable monitoring for critical security events, like integrity violations or debugger detection. Your app should report any signs of tampering directly to your security infrastructure.

Post-deployment monitoring (ongoing)

Effective application security isn’t a one-time project, but an ongoing process that should involve the following post-deployment measures:

• Continuous threat monitoring: Set up alerts for suspicious behavior, such as unusual API call patterns or repeated integrity check failures. These signals can help you detect exploitation attempts early.
  
• Vulnerability management: Define a clear process for assessing and patching newly discovered vulnerabilities. Include criteria for when to issue emergency fixes and how to prioritize updates.
  
• Regular security reassessment: Threats evolve, and so should your defenses. Review your most sensitive components at least quarterly to ensure existing protections are still effective.

Application security example

To see the potential impact of building security into every stage of the SDLC, let’s walk through a hypothetical scenario involving a fintech company protecting one of its most sensitive workflows: the login flow of a mobile banking app.

Scenario: MobileSafe, a digital banking platform serving over 400,000 customers, was facing growing threats from credential-stuffing attacks and APK tampering in its mobile app.

Steps taken

• Threat assessment and asset identification: The security team conducted a detailed threat modeling session focused specifically on the login flow. They discovered that attackers could reverse engineer the biometric validation logic to create bypass methods or extract API endpoints to perform server-side brute force attacks.
  
• Development-time protections: The bank’s DevOps and security teams collaborated to implement several code-level defenses. They created time-limited authentication tokens with proper expiration validation and deployed certificate pinning for all API communications to prevent man-in-the-middle attacks.
  
• Build-time hardening: The teams applied targeted protections to the sensitive components they had identified. These included code obfuscation to rename all classes and methods in the authentication module, dead code insertion to complicate static analysis, and string encryption for all authentication API endpoints.
  
• Runtime protections: To further strengthen security, MobileSafe implemented multiple layers of runtime protection, including anti-tampering measures, anti-debugging techniques, and real-time detection of hooking frameworks such as Frida and Xposed.
  
• Monitoring and response: As a final step, Mobile Safe implemented automated API blocking for devices exhibiting tampering patterns, along with anonymous security telemetry to detect and report attempted breaches.

Results

Following the steps above, MobileSafe achieved:

• 44% reduction in suspicious authentication attempts
• Complete elimination of reported credential-stuffing incidents
• Maintained full compliance with PCI-DSS and GDPR requirements
• Preserved strong app performance and user experience

By taking a layered, proactive approach, MobileSafe protected its code, safeguarded customer assets, and strengthened its overall security posture.

Layered security: Combining development and runtime protections

Even with strong development-time strategies like static application security testing (SAST), the threat landscape is always evolving. That means early efforts—while essential—won’t catch everything. To truly protect your application, you need a layered approach that combines both development-time and runtime defenses.

Why layering matters

A layered security strategy ensures that even if a vulnerability slips through during development or a zero-day exploit appears, runtime protections can detect and respond to threats in real time. This dual-layered model doesn’t just improve resilience. It also increases the complexity and cost for attackers, giving your team more opportunities to detect and neutralize malicious activity.

How layers work together

A layered security strategy reduces the impact of any single vulnerability and increases the complexity and cost of successful attacks. It creates multiple checkpoints where threats can be detected and neutralized, often before they can do damage.

For example:

• Development-time obfuscation makes it harder for attackers to locate critical logic.
• Runtime integrity checks block tampering attempts.
• Anti-debugging tools stop reverse engineering in real time.
  

If an attacker attempts to bypass code protections using static analysis, they’ll trigger runtime defenses. If they try to disable those defenses, their tools are blocked, and your monitoring system is alerted. Even zero-day attacks can be surfaced and studied to build new rules that prevent repeat exploits.

Implementing layered protection

To create a layered security posture, you’ll need to apply different techniques across both development and runtime phases.

During development:

• Follow secure coding practices (e.g., input validation, output encoding, proper error handling).
• Use threat modeling to analyze your app from an attacker’s point of view.
• Apply post-build obfuscation techniques like:
  • Name mangling
  • Control flow flattening
  • Dead code insertion

During runtime:

• Implement anti-tamper mechanisms that detect and respond to unauthorized code modifications.
• Use string encryption to protect hardcoded secrets, even if attackers break through earlier defenses.
• Apply telemetry to monitor system behavior and user activity in real time to detect anomalies and trigger response actions.

The table below compares development vs. runtime protection to solidify your understanding of how development-time and runtime AppSec measures complement each other in enhancing the security of your apps:

	Development-Time Protection	Runtime Protection
Timing	Applied during code writing and the build process	After deployment
Primary Purpose	Prevent code analysis and understanding	Detect and respond to active attacks
Key Techniques	Code obfuscation, dead code insertion, control flow flattening, string encryption	Integrity checking, anti-tamper, environment validation, RASP
Ownership	Development team with security guidance	Security team with DevOps support
Implementation	Integrated into the source code	Embedded within runtime code
Strengths	Makes reverse engineering difficult and costly	Detects and responds to zero-day attacks
Limitations	Static protection can eventually be bypassed	May impact app performance without proper optimization

Best practices for defending your applications

Even with layered protections in place, there are additional steps you can take to strengthen your application security strategy. These best practices can help you prioritize your efforts, minimize risk, and respond more effectively when threats arise.

Prioritize protection based on asset value

Not all code requires military-grade application security. Use a tiered approach to focus your efforts where they’ll have the most impact:

• Tier 1 (Highest protection): Authentication logic, cryptographic implementations, license validation, proprietary algorithms
• Tier 2 (Enhanced protection): Payment processing, personal data handling, business logic rules
• Tier 3 (Standard protection): UI components, non-sensitive features, diagnostic functions

This strategy helps balance strong security with performance and development efficiency.

Enforce stringent authentication controls

Users can unintentionally put your application at risk—through weak passwords, credential reuse, or phishing. Enforcing multi-factor authentication (MFA) or biometric authentication helps add critical friction for attackers, even if one layer is compromised.

Create and deploy a security monitoring strategy

Monitoring isn’t just for runtime, it’s an essential part of your overall defense. Make sure to:

• Set up anomaly detection for suspicious behavior
• Regularly review security telemetry data
• Use canary values or traps to detect probing or tampering attempts

Continuous visibility into what’s happening inside your app gives you the power to respond before small issues become full-blown breaches.

Prepare for security failures

Even the most secure systems can be compromised—hat matters is how quickly and effectively you respond. Make sure to:

• Develop and regularly test your incident response plan
• Conduct security simulations to train your team
• Implement containment strategies, like blocking compromised sessions or isolating affected services

Being prepared minimizes impact and accelerates recovery when something goes wrong.

Bottom line

Application security isn’t something you can bolt on at the end. It needs to be thoughtfully designed, actively implemented, and continuously improved across development, deployment, and beyond. By combining secure coding practices with runtime protections and ongoing monitoring, you give your software the resilience it needs to stand up to today’s evolving threats. PreEmptive helps development and security teams build layered defenses directly into their applications, from obfuscation and encryption to runtime checks and tamper detection. If you’re looking to strengthen your app security without sacrificing performance or user experience, explore how PreEmptive can support your team’s security strategy with a free trial!