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Aleksander Furgal Published: 7 Jul 2023 14 min to read

Website Security Audit: 15 Best Practices and Software Recommendation

According to a report published in 2022, 95 percent of cybersecurity breaches are caused by human error.

Furthermore, 68% of business leaders feel their cybersecurity risks are increasing, highlighting the urgency of conducting regular website security audits.

Despite these concerns, statistics paint an alarming picture – only five percent of companies’ data is properly protected, leaving the vast majority of businesses vulnerable to cyberattacks, data breaches, and potential financial and reputational damage. Moreover, 54 percent of companies admit that their IT departments are not sophisticated enough to handle advanced cyberattacks, further emphasizing the need for external expertise and tools in conducting a website security audit.

In this article, we will delve into the intricacies of a website security audit, providing you with a roadmap to identify vulnerabilities, implement robust security measures, and ensure the ongoing protection of your digital assets. Armed with this knowledge, you will learn how to lead your organization towards a more secure digital future.

What is a Website Security Audit?

A website security audit is a comprehensive evaluation of a website’s entire ecosystem aimed at uncovering vulnerabilities susceptible to attacker exploitation.

This in-depth examination includes critical components like the core system, extensions, server environment, Secure Sockets Layer (SSL) connections, themes, and plugins. By ensuring that all concealed weaknesses are detected and addressed, a website security audit fortifies the website’s defenses, providing an enhanced level of security.

A website security audit not only identifies vulnerabilities but also provides guidance on remediation strategies, aligns the website’s security measures with industry standards, and supports compliance with relevant laws and regulations. This comprehensive process is critical to maintaining a secure, robust online presence, thereby safeguarding your organization’s reputation and customer trust.

# Website security audit vs. website penetration testing

Website security audits and website penetration tests are often mistakenly conflated together.

However, they serve different yet complementary roles in the broader scope of website security. While a penetration test is a targeted practice that simulates cyber-attack scenarios to identify potential vulnerabilities, a website security audit is a more extensive procedure.

Website security audits include penetration testing as one of their elements but also encompass broader assessments of security policies, user access controls, and other facets of the website’s security architecture.


What are the major benefits of a Website Security Audit?

There are several benefits that result from undertaking a website security audit, and these include the following;

  • It helps assess website’s security performance
    A website security audit assesses website security performance against set criteria. It pinpoints areas that may be degrading the website’s overall performance, allowing security architects to focus on such areas to enhance performance.
  • It validates website’s security posture
    Another benefit of a website security audit is that it verifies its resilience and validates its security posture. A website security audit informs security professionals whether the organization’s security measures are in place and, if so, whether they are adequate.
  • It minimizes website’s security risks
    A website security audit proactively searches for vulnerabilities in the website’s architecture. It reduces the probability of damage and chances of noncompliance risks that come in the form of fines and other penalties.
  • It reduces website’s interruptions
    Discovering website vulnerabilities early reduces the chance of disruption to existing website operations, including transactions and payment processes. By auditing your website security, you can ensure that your website’s performance is maintained throughout.
  • It boosts user trust and confidence
    Carrying out website security audits allows the organization to build and maintain customer confidence and trust. Customers can interact with the website without fearing for their safety, security, and privacy.
  • It prevents data leakage
    A properly performed website security audit is an effective mechanism for preventing data leakage by identifying configuration, development, and logic problems and resolving them.
  • It enhances threat intelligence
    Website security audits equip organizations with insights into the exploitability and severity of each identified vulnerability, as well as the potential consequences of successful exploits. Acquiring such knowledge gives organizations a first-mover advantage over attackers by securing the website before they locate and exploit the vulnerabilities.
  • It results in significant cost savings
    Conducting a website security audit saves money long-term by preventing attacks and data breaches that can affect the organization’s operations and, consequently, its revenue-generating capacity. Moreover, prevention costs are typically significantly lower than detection and recovery costs.
  • It resolves problems with security policies and protocols
    By undertaking a website security audit, you can discover problems related to the organization’s security policies. The policies can then be adjusted in order to strengthen the organization’s overall security posture.


A common misconception is that implementing high-tech solutions alone guarantees security, while in reality, consistent processes and an educated workforce are equally vital. We strongly advise companies to approach website security holistically, acknowledging that it’s not just about patching vulnerabilities, but also about nurturing a culture of security-awareness and embedding robust, regularly reviewed security practices into every facet of their digital operations. Paul Jackowski CEO, ASPER BROTHERS Let's Talk


Who should be in charge of a Website Security Audit?

Depending on the requirements, website security audits can be performed by either internal or external auditors. It’s important to note, however, that some organizations may have blended arrangements, where internal auditors do frequent audits and external auditors become involved periodically.

In any case, external auditors typically rely on the internal audit team while conducting their independent investigations. Hence, the two types of audits are interlinked. The table below shows a detailed comparison between internal and external website security audits.

Internal External

Organization’s own security team or employees.

Third parties with no prior links to the organization.


Less objective, as internal personnel usually has prior knowledge of organizational systems.

More objective and less biased. An independent party has no knowledge of organizational systems.


More conducive to white box testing as they expose source code to internal teams.

More conducive for black box tests from an attacker’s perspective.


Conducted on a frequent basis.

Performed less frequently.


15 best practices for a successful Website Security Audit

The following section contains a thorough assessment of practices, designed to identify vulnerabilities and strengthen a website’s defense mechanisms.

They cover a broad range of strategies, from regular configuration testing and updates to implementing robust incident response plans.

By adhering to these best practices, you can bolster your organization’s security posture, protect sensitive data, and instill trust into your digital interactions.

#1 Regularly perform website configuration and penetration testing

As part of the website security audit, review the website’s configuration settings for possible vulnerabilities. Ensure only intended content is displayed to users, establish secure file permissions, and check for blacklisting status. Examine for malware, errors, and outdated software. Ensure spam is eliminated and all backend information is concealed. Conduct vulnerability assessments and penetration tests, and ascertain all vulnerabilities are addressed.

To boost security further, consider continuous monitoring for unusual activity, regular checks of the integrity of website files, and keeping an updated inventory of all website assets. This continuous vigilance and comprehensive understanding of the website’s components contribute to a robust defense against potential threats.


#2 Keep your tech stack and web infrastructure elements up to date.

Outdated tech stacks and web infrastructure can harbor vulnerabilities, inviting potential attacks. Thus, regularly updating extensions, plugins, themes, and software is crucial to reduce security breach risks. Ensure all vital files are updated whenever a new version of a website component or software is released, as most exploits target outdated software. Software patches are also valuable in addressing these vulnerabilities. Maintain all plugins in their most updated state.

To further improve security, consider setting up automatic updates where possible, carrying out regular audits of installed software, and removing unnecessary or obsolete plugins or software. This proactive approach aids in mitigating potential threats by maintaining up-to-date security measures.


#3 Ensure configuration and deployment practices.

During a website security audit, check if the domain or IP addresses are blacklisted, and if so, report to the hosting provider for removal. Confirm the installation of Intrusion Detection Systems/Intrusion Prevention Systems (IDS/IPSs) to deter intrusions. Ensure all code is deployed in a test environment first to avoid disruption to the live website, testing all features without compromising website availability. Only apply changes to the live website once everything functions correctly.

For a more comprehensive security strategy, consider employing automated scanning tools for blacklist checks, continuous monitoring and alerting systems for intrusions, and a structured code deployment and testing process. These tools allow for prompt detection and resolution of potential issues, ensuring seamless operation of the live website.


#4 Evaluate your brute force attack prevention methods

During a website security audit, evaluate the website’s password architecture and ensure controls preventing brute force attacks are in place. Confirm the use of unique, strong passwords that are regularly updated, password managers for secure storage, and limits on login attempts. Implement Single Sign-On (SSO) and Multi-Factor Authentication (MFA). Secure protocols like Secure Shell (SSH) or Secure File Transfer Protocol (SFTP) will further enhance security.

For additional protection, consider periodic user training on the importance of password security, employing a system of regular prompts for password updates, and integrating additional layers of encryption for data transfers. This holistic approach toward password management can significantly minimize the chance of potential breaches.


#5 Remove all inactive user accounts

Inactive user accounts, prone to compromise and serving as potential undetected entry points for attackers, can create security loopholes. They may reuse passwords, lack multi-factor authentication, and miss security validation. Eliminating these accounts during a website security audit is key to minimizing the website’s attack surface.

To further enhance security, it may be beneficial to implement automatic deactivation or deletion policies for dormant accounts and routinely perform audits of active accounts. Doing so will help maintain a cleaner, more secure user base while reducing the possibility of unnoticed breaches.


#6 Analyze website server logs

Automatically generated and stored website server logs capture all requests to the server. Analyzing these logs during website security audits offers multiple benefits: pinpointing issues, tracking user behavior and trends, and providing insights into optimizing performance. Crucially, it also distinguishes potential security issues from performance problems, aiding in their appropriate resolution. These logs can also serve as a valuable source for incident response and forensic investigations in case of actual security breaches.


#7 Guarantee input validation

Input validation aims to confirm data’s correct formatting and validity before it integrates into the system workflow. This practice helps avoid insecure, invalid data entries that may disrupt downstream processes. It’s essential to implement input validation across all website sections, permitting only valid inputs. Security auditors should ensure early-stage input validation in dataflow, particularly at the forms stage. Effective input validation can prevent attacks like Cross-Site Scripting (XSS) and SQL injection.


#8 Verify SSL certificates

A website security audit must confirm the presence and regular renewal of a Secure Sockets Layer (SSL) certificate. By encrypting sensitive website-transferred information, SSL adds a significant layer of security to data exchanges. It’s crucial to maintain vigilance regarding the SSL’s renewal date by monitoring its expiry.

For enhanced security, it’s also advisable to automate SSL certificate renewal processes and establish timely reminders to ensure the certificate never lapses, maintaining the security of data transfers at all times.


#9 Check for protection against SQL injection attacks

During a website security audit, it’s paramount to safeguard the site from SQL injection attacks, in which attackers insert malicious SQL statements into input fields that the SQL database executes. For robust protection against these attacks, ensure all software is updated, withhold database passwords, apply the Principle of Least Privilege (POLP) for database access, and enforce rigorous input validation.

For an even more comprehensive defense, consider employing parameterized queries or stored procedures, instating regular monitoring and logging activities, and deploying a web application firewall to detect and prevent SQL injection attacks.


#10 Review protection against Cross-Site Scripting (XSS) attacks

Cross-Site Scripting (XSS) attacks involve attackers posing as users to access their data and mimic their functions. During website security audits, protective measures such as data sanitization on input, data encoding on output, escaping user input, and implementing a Content Security Policy (CSP) are assessed. By blocking websites from accepting incoming scripts, a CSP can effectively thwart XSS attacks.

To further bolster security, keep software up-to-date, regularly monitor and log activities, and employ a web application firewall to proactively detect and prevent XSS attacks, emphasizing the importance of a comprehensive, multi-layered defense strategy.


#11 Confirm the use of a Web Application Firewall

As part of a website security audit, verify the presence and correct configuration of a Web Application Firewall (WAF). This tool safeguards web applications by monitoring, filtering, and blocking malicious website traffic, serving as the initial line of defense to ensure website availability and integrity. The WAF should be strategically positioned inline before the backend network and can also operate as a reverse proxy, acting as a go-between for clients and the backend network. In this setup, applications can only communicate through the WAF, preventing direct communication with the website server.

To further enhance security, it’s crucial to routinely monitor and update the WAF’s rule sets, ensuring it can detect and mitigate the latest web-based threats, thereby optimizing the website’s defense mechanisms.


#12 Ensure secure backup storage

Website security audit procedures mandate frequent backups to mitigate website recovery failures in potential disasters. These backups facilitate swift recovery upon detecting suspicious activities. Automating and scheduling backups, and diversifying backup locations and methods, can further reduce risks in case a disaster impacts the backup location. Ensuring secure storage of backups and their regular testing can prevent delays during recovery procedures.

To further enhance security and reliability, consider employing backup validation checks and encryption for stored backups. Doing so not only ensures the usability of the backups in case of disaster recovery but also adds an extra layer of security to protect the backup data.


#13 Check if HTTPS is implemented

Employing HTTPS for all pages on your website is a vital security measure that ensures all communication is encrypted, protecting against eavesdropping and tampering. HTTPS, short for Hypertext Transfer Protocol Secure, uses an SSL/TLS protocol to provide a secure connection, which is particularly important when handling sensitive data like login credentials and payment details. During a website security audit, verify that HTTPS is not just available but enforced, ensuring all data exchanges between the website and its users are secure.

For an added level of security, consider incorporating HTTP Strict Transport Security (HSTS) into your website’s security configuration. HSTS instructs web browsers to only connect to your website using HTTPS, preventing certain types of attacks and enhancing the overall security of data transmission.


#14 Confirm access restriction

Restricting access is critical in securing a website and minimizing potential threats from unauthorized access. Implementing POLP is a central part of this process, ensuring that users, systems, and processes can only access the information necessary to perform their functions and nothing more. During a website security audit, it’s vital to confirm that access restrictions are appropriately configured and consistently applied.

In further tightening access controls, consider implementing role-based access control (RBAC) strategies, which define access levels based on user roles within your organization.


#15 Review the Incident Response Plan

An effective Incident Response Plan (IRP) is critical to swiftly and efficiently address security breaches or attacks. It outlines the procedures to follow when an incident occurs, aiming to limit damage and reduce recovery time and costs. As part of a website security audit, verify that a comprehensive IRP addressing all potential scenarios is in place.

To enhance an IRP, consider incorporating elements such as a clear communication strategy, roles and responsibilities during an incident, a plan for isolating systems affected by a breach, and a comprehensive post-incident review process. Regular testing and refining of the IRP is also crucial to ensure it remains effective and up-to-date with evolving threats and vulnerabilities.


Website Security Auditing tools

Website security audit tools streamline the audit process, automating the tasks of scanning, monitoring, and analyzing the website’s security posture. Their capabilities allow for more efficient and effective audits, illuminating vulnerabilities that might otherwise remain hidden. Utilizing them can significantly bolster your website’s defenses.

These tools come in a variety of forms, each with its distinct features and focus areas. Below, we delve into some of the most potent and trusted ones available.

# Sucuri SiteCheck


Sucuri SiteCheck is an exceptional, free-of-charge tool for website security audits. It meticulously scans a website, particularly the source code, searching for malware. Sucuri SiteCheck can verify a website’s blocklisting status, pinpoint errors, and identify outdated software. Additionally, it checks for spam and website defacements, contributing to a comprehensive security overview.

One significant advantage of Sucuri SiteCheck is that beyond threat identification, it offers actionable recommendations for bolstering the website’s defenses. Its efficacy in assessing input validation makes it an indispensable tool in mitigating common security risks such as Cross-Site Scripting (XSS) and SQL Injection attacks.


# Qualys SSL Server Test


Qualys SSL Server Test is a widely used tool primarily focused on verifying website SSL certificates. It thoroughly scans a website for any misconfigurations or vulnerabilities within the SSL framework, grading the website based on a comparative scale that includes the best and worst test scores from recently scanned websites.

The tool provides invaluable information for website security auditors, revealing details about the website’s protocol support level, cipher strength, and key exchange and distribution quality.

One of the primary advantages of Qualys SSL Server Test is that it’s free, making it accessible to a wide range of users. Furthermore, it’s extremely user-friendly; after the user inputs their hostname and hits submit, the tool provides a detailed summary of the SSL audit, including the website’s scores.


# Intruder


Intruder stands as an advanced vulnerability scanner, meticulously examining web applications for prevalent security issues like bugs, configuration weaknesses, and missing patches. With its capacity to analyze website configuration and deployment practices as well as conduct penetration testing, Intruder proves to be a versatile addition to the website security toolkit.

Among the primary advantages of Intruder is its comprehensive scanning capacity, which encompasses all security layers of the website. This tool goes beyond simple detection, providing detailed security assessment reports in line with major security standards and frameworks, including PCI DSS and ISO/IEC 27001. Such compliance ensures that your website security measures meet universally recognized benchmarks.

However, a significant limitation of Intruder is its lack of a free version, which might be a barrier for some. Nonetheless, given its extensive features and capabilities, it is a worthwhile expenditure for enhancing your website’s security posture.


# SiteGuarding


SiteGuarding is a robust website security audit tool designed to provide continuous, round-the-clock monitoring and analysis of websites. Upon identifying potential issues, this proactive tool takes immediate measures to rectify the problems, ensuring continuous, uninterrupted operation of your website in a secure environment.

One of the significant attributes of SiteGuarding is its ability to respond and adapt quickly to potential security threats. Whether it’s an unexpected downtime, a suspicious activity, or detected malware, SiteGuarding addresses these issues promptly, limiting potential damages and ensuring your website’s security.


# NordPass


NordPass is widely regarded as the best password security manager. This tool facilitates robust password hygiene, acting as a vital deterrent against password attacks like brute force intrusions.

NordPass generates unique passwords, safely storing them in encrypted vaults that can be conveniently accessed via your website browser. This feature effectively reduces the risk of unauthorized access and enhances overall website security.

One of the main advantages of NordPass is its support for encryption and MFA. Furthermore, NordPass allows for automatic backups and biometric authentication, amplifying its security prowess.


# Splunk


Splunk is used for deep-dive log analysis and continuous monitoring during a website security audit. It plays a crucial role in identifying, troubleshooting, and managing website server logs.

The tool is designed to meticulously gather, monitor, and analyze website server logs, enabling you to swiftly pinpoint and resolve any potential issues. Once a problem is detected, Splunk not only facilitates the resolution but also diligently oversees the implementation of the remedy. This could involve updating the website code, adjusting website server configurations, or applying necessary security patches to bolster security.

One of the standout features of Splunk is its ability to generate built-in alerts and reports, providing a comprehensive overview of the system’s status. Moreover, its user-friendly dashboards and unique visualizations offer a clear, simplified view of complex data, making problem detection and resolution more accessible and efficient.



Conducting a website security audit is a key step in protecting your website from cyber threats. These audits are proactive, meaning they help find and fix potential issues before they become real problems.

The role of website security auditors is crucial, as it is the auditing personnel that, equipped with tools and knowledge, forms the foundation of a successful audit.

But remember, doing a website security audit isn’t just a one-time thing. It’s a continuous process that should be part of your ongoing strategy. Regular audits will help you ensure that your website stays safe as cyber threats continue to change and grow. By sticking with this strategy, you can help build a safer space for your users.


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If conducting a website security audit still seems overwhelming, don’t hesitate to reach out. Our seasoned security experts are here to offer free advice tailored to your specific needs.

Aleksander Furgal

Content Specialist



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