Application Security Controls: The Complete Guide

In June 2024, hackers breached Levi Strauss & Co. and gained access to more than 72,000 customer accounts using a credential stuffing attack. The hackers took advantage of poor authentication controls, getting their hands on personal details, order history and partially encrypted credit card data, leading the company to incur costs around remediation and emergency security defenses.

Worldwide, the average cost was $4.88 million with companies needing 258 days to identify and contain the data breaches, IBM revealed in its 2024 Cost of a Data Breach Report. With 44% of all breaches in 2025 expected to be ransomware and cyberattacks growing 30%, year over year, organizations can no longer afford to merely patch their application security as an afterthought. Let’s examine the various types of application security controls and how to use them correctly in your environment, as well as offer a set of best practices for developers and DevOps teams.

Key highlights:

• Application security controls are essential safeguards that restrict applications from operating in ways that put organizational data at risk, covering authentication, encryption, input validation, and access management.
• Comprehensive application security controls can reduce breach identification time by 98 days and save organizations nearly ~$2.2M compared to those without proper security measures.
• Modern frameworks like NIST CSF 2.0, HITRUST, and ISO/IEC 27034 provide standardized approaches to managing application security risks while maintaining regulatory compliance.

What Are Application Security Controls?

Application security controls are limitations on the application that determine what can operate and how to minimize any threats or risks and maintain the confidentiality of sensitive information.

These controls include not only technical (design and implementation methods) but also policies and procedures for ensuring secure operation of the software in each phase of its lifecycle, from development through deployment and ongoing maintenance, such as the security mechanisms that encompass authentication schemes, encryption technologies, access level restrictions, proper input handling and validation routines or robust monitoring capabilities.

Importance of Application Security Controls for Organizations

• Prevent Data Breaches and Financial Losses: Strong controls prevent organizations from falling victim to expensive data breaches, costing millions of dollars in lost revenue, fines, and remediation. With the average breach costing organizations $4.88 million worldwide, investing in appropriate security measures delivers a substantial return on investment through preventing access to sensitive customer data and business-critical data.
• Maintain Regulatory Compliance: Businesses need to adhere to strict standards such as GDPR, HIPAA, PCI DSS and SOC 2 (based on industry). Application security controls supply a set of technical protections necessary for compliance, enabling organizations to not only avoid large penalties but also demonstrate to regulators how they practiced due diligence in securing sensitive data.
• Protect Brand Reputation and Customer Trust: Security breaches can destroy a brand’s reputation and undermine customer trust – forever. Resilient application level security controls are a strong indicator of how seriously the company takes protecting customer privacy and data. Strong controls are a selling point for customers who, in an age of heightened security awareness, seek out their most trusted online partners.
• Enable Secure Digital Transformation: As enterprises embrace cloud-native architectures, APIs and microservices, application security controls are necessary to enable innovation safely. These controls let organizations embrace modern technology and still stay secure, so digital transformation does not introduce undue risk.
• Reduce Attack Surface and Improve Resilience: Rigorous application security controls reduce exposure by closing attack vectors, enforcing privilege access, and following in-depth defense tactics. This layered strategy ensures that if one control fails, an attacker doesn’t instantly gain complete access.

Application vs Software Security Controls: What’s the Difference?

Application security controls focus on runtime environments and operational behaviors within deployed applications, such as how applications interact with users, process data, or communicate with other systems, covering authentication, authorization, and session management for production.

Software security controls focus on the development lifecycle, in which code security is incorporated into secure coding practices, code review processes, static analysis, dynamic analysis, and vulnerability assessment to secure code. Software security addresses vulnerabilities prior to production, while application security defends during execution.

Types of Application Controls

Completeness Checks: Require all necessary data fields and information to be present before performing transactions or requests. They control what needs to be input for applications to work properly, which is important as mistakes here can lead to security vulnerabilities or system failures. Completeness checks are validation checks to ensure that mandatory fields, required uploads of files and prerequisite conditions for the attack were established in order to mitigate incomplete transactions that attackers can exploit.

Validity Checks: Verify that variables’ values are of the expected type and range before processing them. These inputs validate e-mail structure, date spans, numeric bounds and patterns of input. Input validation shields against injection attacks, buffer overflows, and other input-related vulnerabilities caused by malformed data in the input, which allows only properly formed data to enter systems..

Identification: Verify the identity of those who seek access to resources on the user, system or application level. These controls generate unique identifiers for assigning identities, retain identity repositories and keep track of identity management across all stages of application development, with the intention to support access control decisions and audit trails for accountability.

Classification: Classify data and resources according to sensitivity, impact, and protection level required. These controls tag data in accordance with organizational policies and necessary regulations, allowing applications to enforce security measures based on the classification of information, thereby preventing loss of data and ensuring that sensitive content will be protected.

Logging: Capture and record application events, user activities, security incidents, and system operations for analysis and audit purposes. Comprehensive logging provides visibility into application behavior, enables threat detection, supports incident response, and maintains audit trails for compliance, capturing authentication attempts, access requests, and suspicious activities.

Encryption: To protect data confidentiality, the process of converting data into an unreadable format using cryptographic methods is used. These controls protect stored data, data being transferred over a network, and data used during processing. Proper encryption of data can prevent unauthorized access even if attackers penetrate other perimeter defenses such as good key management and algorithm selection.

Authentication: Authentication ensures that users (and systems) are actually who they say they are before allowing them access. These controls include multi-factor authentication, password policies, biometric checks, and single sign-on to allow only trusted users access while stopping impersonation-based unauthorized entry, account takeovers, and credential attacks.

Access Controls: Determine what authenticated users and systems can do within applications by enforcing authorization policies and permissions. These controls implement role-based access control (RBAC), attribute-based access control (ABAC), and the principle of least privilege, preventing privilege escalation, unauthorized data access, and lateral movement by attackers.

Input Controls: Treat all input as malicious. Validate (whitelist) and sanitize (blacklist) input, use safe API, escaping, or place an application firewall in front of the application if possible to prevent injection attacks, cross-site scripting attacks, etc. Such controls validate input strings against malicious patterns, deny requests containing malicious data, and block unexpected message formats, thus preventing SQL/command injection or attacks due to improper input handling.

Output Controls: Ensure applications properly encode and sanitize data before displaying it to users or sending it to other systems. These controls prevent cross-site scripting attacks, information disclosure, and data leakage by properly formatting output based on context, masking sensitive data and implementing error handling that doesn’t reveal system details.

Benefits of Application Controls for Your Team

Implementing comprehensive application security controls delivers measurable advantages that strengthen security posture while enabling business objectives. These benefits extend across security, operations, and business functions, providing value to multiple stakeholders throughout the organization.

Understanding Application Control Frameworks

• NIST CSF: The NIST Cybersecurity Framework version 2.0, last updated in 2024, offers a holistic set of guidance centered around six key functions (Govern, Identify, Protect, Detect, Respond and Recover), which are all transformed based on an organization’s risk profile.
• HITRUST CSF: The HITRUST Common Security Framework consolidates more than 60 regulations and standards into a single, prescriptive framework for consumers while providing a 99.41% cumulative breach-free rating in HITRUST-certified environments; thus, streamlining the compliance process.
• Cloud Control Matrix (CCM): The Cloud Security Alliance’s CCM version 4.0 is a standardized set of cloud security controls covering technical and organizational measures that serve as international control standards mapping to many leading standards globally.
• CMMC 2.0: The Cybersecurity Maturity Model Certification 2.0, effective December 2024, establishes three compliance levels based on NIST standards for Defense Industrial Base contractors handling Federal Contract Information.
• ISO/IEC 27034: This international standard includes the processes that manage the application security and it incorporates some concepts like the Organization Normative Framework and Application Security Controls with the purpose of promoting security in all development processes.

Implementing Application Controls: Key Steps

Conduct a Comprehensive Asset Inventory

Develop a comprehensive catalog that lists all applications, their API, and dependencies within your company. Record application owners, business impact, data sensitivity levels and any current security controls for each asset.

• Include cloud-based and on-premises applications
• Document third-party and custom-developed software
• Identify APIs and integration points
• Track mobile applications and web services
• Maintain inventory as a living document with continuous updates

Perform Threat Modeling and Risk Assessment

Perform structured threat modeling to recognize possible attack vectors, weaknesses, and threats unique to an application. Apply frameworks such as STRIDE or PASTA in systemic analysis of security threats.

• Identify critical assets and sensitive data requiring protection
• Map data flows and trust boundaries within applications
• Evaluate the likelihood and potential impact of identified threats
• Prioritize risks based on business context and exploitability
• Document findings to inform control selection

Integrate Security into the Development Lifecycle

Apply DevSecOps techniques to bake security into your systems instead of treating it as a last-minute gate. Execute security tasks at each phase of the SDLC.

• Conduct architecture reviews during the design phase
• Provide secure coding training and static analysis tools in development
• Perform dynamic testing and penetration testing during the testing phase
• Use automation to enforce security checks without slowing development

Implement Authentication and Authorization Controls

Implement strong authentication mechanisms that validate user identity before granting access.

• Enforce strong password policies with complexity requirements
• Implement MFA using multiple verification factors
• Deploy single sign-on for improved user experience
• Add adaptive authentication based on risk factors
• Implement secure session management preventing hijacking

Deploy Input Validation and Output Encoding

Use really good input validation that examines everything coming into apps before processing it. Develop allowlists of valid input patterns, not just blocklists.

• Verify data types, formats, lengths, and ranges
• Sanitize special characters and reject malicious payloads
• Validate file uploads including content type verification
• Implement context-aware validation based on data usage
• Reject unexpected or malformed input entirely

Establish Logging and Monitoring Capabilities

Use application-agnostic, comprehensive logging of security-related incidents. Make sure that logs are detailed enough to be useful in an investigation, while still keeping sensitive data safe.

• Capture authentication attempts and access requests
• Record configuration changes and administrative actions
• Log security exceptions and error conditions
• Protect log integrity through secure storage
• Retain logs according to compliance requirements

Implement Data Protection Controls

Deploy encryption controls protecting data throughout its lifecycle. Encrypt sensitive data at rest using strong algorithms and proper key management. Protect data in transit using TLS 1.3 or higher.

• Implement database encryption for sensitive information
• Use file system and disk encryption where appropriate
• Deploy secure key management with regular rotation
• Add data masking for non-production environments
• Implement data loss prevention to prevent unauthorized exfiltration

Conduct Security Testing and Validation

Perform regular security testing using multiple techniques to identify vulnerabilities before attackers exploit them. Implement both automated and manual testing approaches.

• Use Static Application Security Testing during development
• Deploy Dynamic Application Security Testing in test environments
• Leverage Interactive Application Security Testing combining both approaches
• Conduct penetration testing by skilled security professionals
• Perform Software Composition Analysis for third-party dependencies

Application Security Control Best Practices

Train Developers in Secure Coding Practices: Implement comprehensive security training that equips developers to embed security from the outset. Training should also include OWASP Top 10 vulnerabilities, secure coding practices tailored to your technology stack and how to employ security libraries effectively.

Set Up Processes to Address Software Vulnerabilities: Put in place formal vulnerability management processes that uniformly identify, prioritize, and remediate security issues. Establish firm SLAs on patching by severities, introduce automated scans as part of CI/CD pipelines, have exception processes with compensating controls, and report MTTR & maintain an inventory of all software components.

Use Risk Assessment Methodologies: Standardize on risk assessment methodologies that provide a structured approach for performing consistent and repeatable application security risk assessments. Leverage frameworks such as NIST SP 800-30, ISO 27005 to categorize threats and vulnerabilities in a structured manner, evaluate the probability and severity of possible occurrences, score risks for prioritization purposes, record risk acceptance decisions about these issues and perform assessments before significant business releases are deployed.

Implement Security Logging and Monitoring: Deploy comprehensive logging and monitoring solutions providing real-time visibility into application security events and enabling rapid incident detection. Centralize logs from all applications into a SIEM platform for correlation and analysis, ensuring monitoring includes failed authentication attempts, unusual access patterns, high-volume requests, data exfiltration attempts, and configuration changes to security-relevant settings.

Enforce Access Controls: Apply the principle of least privilege to all system components and services, ensuring that only authorized users are able to access systems. Ensure that all users and systems operate with the least privileges necessary to accomplish legitimate tasks by exercising access reviews on a regular basis, enabling automated deprovisioning when a user’s status changes, utilizing privileged access management for administrative accounts, implementing just-in-time access for temporary process elevation, and using separation of duties for critical operations.

Simplify Application Controls with Cycode

Centralizing the security management of application controls in today’s dispersed development environment has proven challenging for security and development organizations. Cycode’s AI Native Application Security Platform centralizes how controls are implemented, automates security testing, and helps your team ship secure code faster.

Book a demo today and discover how Cycode can help your team manage application security controls better.