E-commerce Security Checklist: How to Ensure Your Website is Safe

Security for e-commerce websites is non-negotiable. As online sales continue to climb, so do the risks. Cybercriminals are evolving, targeting e-commerce platforms with attacks ranging from data breaches and payment fraud to account takeovers and malware injections. According to IBM’s 2024 Cost of a Data Breach report, the average breach cost in the retail sector was over $4.88 million, with reputational damage and customer loss often being far more severe.

For e-commerce businesses, website security directly impacts customer trust, data privacy, compliance, and business continuity. Shoppers expect secure transactions, private data handling, and uninterrupted service. One misstep, and a customer might never return.

This article offers website security tips for e-commerce to help business owners, developers, and IT teams safeguard their websites against evolving threats. Let’s explore the practical steps you can take to ensure your online store is resilient, trustworthy, and compliant.

1. Use HTTPS and SSL Certificates to Encrypt Data

Think about the last time you shopped online. You likely glanced at the browser bar to see that reassuring little padlock next to the URL–proof that the site was secure and encrypted. That padlock, powered by HTTPS and an SSL certificate, is the first visual cue customers look for when deciding whether to trust an e-commerce website with their personal and payment information.

Yet, many e-commerce businesses still overlook or delay the implementation of HTTPS, not realizing that this basic layer of encryption is one of the most critical website security practices in the online retail world.

HTTPS (HyperText Transfer Protocol Secure) encrypts the data exchanged between the customer’s browser and your website, protecting it from being intercepted by cybercriminals during transmission. Without it, your site is essentially an open highway where sensitive information–like login credentials, credit card numbers, and shipping addresses–can be easily hijacked.

Installing an SSL (Secure Sockets Layer) certificate is what enables HTTPS. It’s a small yet powerful upgrade that signals to both customers and browsers that your website can be trusted. And trust matters: according to a recent survey, over 51% of users would abandon a purchase if they saw a safety warning in their browser.

However, the benefits go beyond customer perception. Google has confirmed that HTTPS is a ranking signal, meaning secure sites may enjoy a boost in SEO visibility. Moreover, if your online store accepts credit card payments, using HTTPS is essential for PCI DSS compliance, which mandates encrypted transmission of cardholder data.

How to implement it effectively:

• Purchase an SSL certificate from a reputable Certificate Authority (CA), or use Let’s Encrypt if you're looking for a free, automated option.
• Ensure all pages, not just checkout or login screens, are served over HTTPS to avoid mixed content issues.
• Set up 301 redirects to automatically send HTTP traffic to HTTPS versions of your site.
• Regularly monitor the certificate’s expiration date to avoid unexpected outages or browser warnings.
• Use tools like SSL Labs’ SSL Test to scan your site and ensure your SSL setup is secure and up to date.

2. Keep Your Software Up to Date

If there’s one golden rule in cybersecurity, it’s this: outdated software is an open door for attackers.

Whether it’s your e-commerce platform, plugins, payment gateways, or server OS, running outdated versions puts your website at immediate risk of exploitation.

It’s easy to underestimate the urgency. Updates can feel tedious, and delaying them in a busy e-commerce environment can be tempting–especially if everything appears to be working “just fine.” But under the surface, vulnerabilities are quietly accumulating. In fact, according to a report by the Ponemon Institute, 57% of data breaches were directly linked to known, unpatched security vulnerabilities, many of which had been publicly disclosed months in advance.

For e-commerce websites, the risks are even higher. Outdated software can lead to:

• SQL injections and cross-site scripting (XSS) attacks via vulnerable plugins or forms
• Compromised payment integrations exposing customer credit card data
• Malware infections that turn your site into a phishing or spam host without your knowledge

The truth is that cybercriminals are opportunists. They actively scan the web looking for websites running older versions of popular CMS platforms. Why? Because outdated software often contains publicly known vulnerabilities, exploiting them is often as easy as running a script. Remember, cybercriminals don't target you personally, they target your weaknesses. Don’t give them the opportunity.

E-commerce platforms like Magento, WooCommerce, Shopify, and others frequently release patches that fix security flaws, improve performance, and comply with new regulatory requirements. Third-party plugins, extensions, and themes must also be updated regularly, since these components often serve as entry points for cyberattacks because they’re less rigorously maintained or tested.

Best Practices for Staying Secure:

• Enable automatic updates where possible, especially for critical plugins and core platform software.
• Maintain a staging environment to test updates before deploying them to your live site.
• Create a regular update schedule, and don’t skip it–security doesn’t wait.
• Remove unused plugins, extensions, and themes. Even if inactive, they can pose a threat.
• Subscribe to security bulletins or newsletters for your e-commerce platform to stay informed about urgent patches.

Imagine running your online store on an outdated version of Shopify that hasn’t patched a known security flaw. In the eyes of an attacker, your site becomes an open door. They might inject malicious code, hijack customer sessions, or steal stored data. All without you even knowing until it's too late.

This isn't theoretical. The infamous Magecart attacks, where hackers injected card-skimming malware into thousands of e-commerce sites, often succeeded because store owners hadn’t updated their software in time. And these attacks can happen even if you're using an otherwise reputable e-commerce platform.

What Needs to Be Updated?

• CMS Platforms
• Themes and Templates
• Third-party Plugins & Extensions
• APIs and Payment Gateway Integrations
• Server-side software (e.g., PHP, MySQL, Apache/Nginx)

Pro Tip: If your platform supports it, enable automatic security updates for plugins and themes. Better yet, work with a managed services provider or development partner (like Svitla, wink wink) to maintain a regular patching and testing cycle as part of your DevSecOps or maintenance strategy.

3. Use Secure Payment Gateways to Protect Transactions

When it comes to running a successful e-commerce site, few things are more important, or more sensitive, than processing customer payments. In a world where payment fraud, phishing, and card theft are on the rise, using a secure, trusted payment gateway is no longer optional. It's the cornerstone of a secure transaction ecosystem.

A payment gateway technology captures and transfers payment data from the customer to the acquiring bank. If it’s not properly secured, that transfer becomes an ideal entry point for fraudsters and data thieves looking to intercept credit card numbers, CVVs, and other sensitive information.

Why It’s Critical to Choose the Right Gateway

Not all payment gateways are created equal. Some offer robust encryption, tokenization, fraud detection, and PCI DSS compliance, while others cut corners to save on costs, leaving your customers (and your business) exposed. The consequences? Data breaches, financial penalties, legal liabilities, and a devastating loss of customer trust.

According to recent reports, payment card fraud globally resulted in losses of close to $34 billion in 2023, with e-commerce being a primary target. And once a business is flagged for poor security practices, recovering its reputation can take years. If ever.

So, what should you look for in a secure payment gateway?

• PCI DSS Compliance: Ensure the provider is certified to handle cardholder data securely.
• Tokenization: Converts payment data into secure, non-sensitive tokens so that real card data is never stored or exposed.
• End-to-End Encryption: Protects transaction data throughout the payment process.
• Fraud Detection & Risk Monitoring – Many top-tier providers offer AI-powered tools to detect suspicious activity in real time.
• Secure Hosted Payment Pages: Keeps your site out of scope for PCI by directing customers to externally hosted checkout pages.

Popular, trusted payment gateways like Stripe, PayPal, Authorize.net, Braintree, and Square all offer these features. They’re continuously audited for compliance, maintained by dedicated security teams, and used by millions of businesses globally.

Pro Tip: Storing payment data on your servers is a massive liability. Let the payment gateway handle it. By outsourcing this responsibility, you reduce your PCI compliance scope and dramatically minimize your exposure to breaches.

By integrating a secure, reputable payment gateway, you’re telling your customers: “You can trust us with your information.”

4. Implement Detection and Patching of Vulnerabilities

One of the most common ways hackers breach e-commerce websites is by exploiting known vulnerabilities in unpatched systems. Whether it’s your CMS, server OS, plugins, or third-party tools, each component in your tech stack is a potential entry point for attackers, especially if it hasn’t been updated with the latest security fixes.

According to a recent report, over 25,000 new software vulnerabilities were disclosed last year alone, a record high. Many of these were critical exploits affecting widely-used platforms, plugins, and libraries. Unfortunately, cybercriminals are often faster to act than businesses are to patch. That’s why having a solid patching and vulnerability management plan is critical.

Think of patching like locking your doors. You wouldn’t leave your front door wide open, right? But that’s exactly what happens when a system or plugin with a known vulnerability remains unpatched–it creates a visible, exploitable weakness that automated bots and threat actors are constantly scanning for.

This is especially dangerous for e-commerce businesses that handle customer data, payment details, and order records, which are lucrative targets for attackers.

How to stay on top of it:

• Implement vulnerability management strategy that includes routine scans, staging environments, security bulletins, monitoring alerts, etc.
• Respond proactively to vulnerabilities. Have remediation plans in place along with incident response integration and prioritization strategies.
• Use tools like Dependabot, WPScan, OpenVAS for vulnerability scanning and management.

5. Implement Strong Authentication and Access Controls

Your e-commerce website could be protected by SSL, monitored for vulnerabilities, and patched regularly; but if attackers can log in through weak credentials or over-privileged accounts, all that hard work can go to waste. That’s why strong authentication and access controls are essential components of any secure e-commerce strategy.

Many data breaches aren’t the result of fancy hacking techniques–they’re caused by something as simple as weak passwords or stolen login credentials. According to Verizon’s 2023 Data Breach Investigations Report, over 80% of hacking-related breaches involved stolen or brute-forced credentials.

This is especially risky for e-commerce businesses, where admin dashboards, order systems, inventory databases, and customer accounts are all interconnected. One compromised login–especially from a high-privilege user–can give an attacker access to everything.

Best Practices for Authentication and Access Management

Enforce Strong Password Policies

• Require a combination of upper/lowercase letters, numbers, and special characters.
• Make a mandatory rule to create passwords with a minimum of 12 characters.
• Enforce password expiration and prevent reuse of previous passwords.
• Educate users and staff on avoiding common password mistakes (like "admin123")

Enable Multi-Factor Authentication (MFA)

Adding a second layer of verification – like a one-time code sent to a mobile device – dramatically reduces the chances of unauthorized access, even if credentials are compromised. Platforms like WooCommerce, Shopify Plus, and Magento support MFA natively or through extensions.

Apply the Principle of Least Privilege (PoLP)

Not every employee needs access to everything:

• Assign role-based permissions and restrict administrative access to only those who truly need it.
• Separate customer service, fulfillment, and development access where possible.
• Regularly review user roles and revoke access for inactive or former employees.

Use Secure Single Sign-On (SSO) for Large Teams

For larger e-commerce teams or businesses integrated into enterprise systems, implementing SSO (with secure identity providers like Okta or Azure AD) can centralize login control and make access revocation easier.

6. Back Up Your Website and Customer Data Regularly

In the world of cybersecurity, there’s one universal truth: breaches, outages, and accidents can still happen, even with the best defenses in place. That’s why backups are your ultimate safety net.

A well-secured e-commerce site is still vulnerable to unexpected threats like ransomware, server failures, human error, or even botched updates. Without a reliable backup strategy, recovering from a breach, or even a small technical mishap, could mean hours (or days) of downtime, lost sales, and potentially irrecoverable customer data.

Imagine your site goes offline during peak holiday shopping hours. Or worse, imagine malicious code corrupts your entire product database or wipes out customer order history. If you don’t have recent, clean backups, you’re starting from scratch, and that could cost you thousands. For e-commerce, where even a few hours of downtime can lead to abandoned carts and lost trust, that's a risk you can't afford.

Here's what a sound back-up strategy looks like:

Backup Regularly and Automatically

• Schedule daily (or more frequent) backups, depending on how active your site is.
• Use incremental backups to save time and storage while capturing all changes.
• Ensure that backups cover all critical components: site files, product data, order history, customer records, and CMS configurations.

Use Offsite and Cloud Storage

• Don’t store backups on the same server as your live site–it defeats the purpose.
• Use cloud-based solutions like AWS S3, Google Cloud Storage, or backup services integrated into platforms like Jetpack (WordPress) or Cloud Backup (Shopify Plus).

Test Your Restores

• A backup is only useful if it works. Test your recovery process regularly to ensure your backups are intact, accessible, and complete.
• Simulate restoration scenarios so your team knows what to do in the event of a real emergency.

Encrypt Sensitive Backup Data

Especially if your backups include customer data, make sure they’re encrypted both at rest and in transit to avoid secondary data leaks.

7. Educate Your Employees and Enforce Security Best Practices

You can have the most secure infrastructure, the best plugins, and airtight policies in place, but all it takes is one employee clicking a phishing email or reusing a weak password to undo it all.

According to a Forrester Report, 74% of breaches involved the human element, including social engineering, credential misuse, and insider errors. Translation? Your employees are one of your biggest risks, and one of your best defenses if adequately trained.

Conduct Regular Training Sessions

• Schedule quarterly or biannual security awareness training to keep best practices fresh.
• Include real-world examples of phishing emails, social engineering tactics, and common e-commerce scams.
• Tools like KnowBe4, Infosec IQ, or Curricula can help you simulate attacks and train users to spot red flags.

Define and Document Security Policies

• Make it clear how employees should handle sensitive data, report suspicious activity, or manage permissions.
• Include onboarding and offboarding checklists to ensure access is granted or revoked promptly and properly.

Encourage a Blame-Free Reporting Culture

• Employees should feel comfortable reporting accidental clicks or suspicious behavior without fear of punishment.
• A fast, transparent response can mitigate damage before it spreads.

8. Perform Regular Security Audits and Penetration Testing

You wouldn’t launch a new product without testing it, would you? The same logic applies to your e-commerce website. Security audits and penetration testing (pen-tests or pen-testing) are your opportunity to poke holes in your defenses before hackers do, giving you a clear, actionable view of your platform’s true security posture.

While tools like firewalls and malware scanners are essential, they’re reactive by nature. Audits and pen-tests are proactive; they simulate real-world attacks to identify blind spots, misconfigurations, and vulnerabilities that automated tools might miss.

So, what’s the difference between security audit and a penetration testing?

Security audit is a comprehensive, systematic review of your codebase, configurations, third-party integrations, and compliance readiness. Think of it as a high-level risk assessment.

Penetration testing is an ethical hacker’s attempt to exploit your systems the way a real attacker would, uncovering practical vulnerabilities in your infrastructure, authentication flows, APIs, and business logic.

Here’s how to get started with both:

• Partner with trusted security experts to run manual and automated assessments tailored to e-commerce platforms.
• Choose firms familiar with Magento, Shopify Plus, WooCommerce, or your custom tech stack.
• Run a full security audit at least once per year or after any major system update.
• Schedule penetration testing biannually, or more frequently if you handle high volumes of sensitive data.

9. Implement a Web Application Firewall (WAF)

The purpose of a Web Application Firewall (WAF) is to protect web applications from hackers by filtering and monitoring HTTP and HTTPS traffic. Basically, it’s like a barrier between carefree users and web apps that blocks away any malicious traffic and activity.

WAF protects your e-commerce website from several major threats, including:

• Top 10 vulnerabilities according to OWASP, including SQL injections, broken access control, and security misconfiguration.
• Distributed Denial of Service (DDoS) attacks
• Automated bot attacks

10. Set Up a Content Security Policy (CSP)

The purpose of a Content Security Policy (CSP) is to protect web applications from cross-site scripting attacks (XSS) and code injection attacks by restricting the sources of content. By specifying trusted domain names for scripts, images, and styles, the CSP policy prevents malicious code scripts from running on your website, data breaches, and unauthorized modifications.

Implementing the CSP policy is critical not only in the e-commerce field, but in any websites or platforms that handle financial transactions, manage user data, or simply carry sensitive information.

11. Comply with Data Protection Regulations

Security isn’t just about defending against threats; it’s also about doing things the right way. E-commerce businesses must comply with a growing list of data protection and privacy regulations that govern how customer data is collected, stored, used, and protected.

Failure to comply invites and erodes customer trust. Shoppers want to know their personal data is handled responsibly. And regulators? They want proof.

From GDPR in Europe to CCPA in California and PCI DSS for payment processing, compliance is no longer optional. It’s a legal and ethical obligation.

Key E-commerce Compliance Standards

Steps to Stay Compliant

• Know what you collect. Conduct a data inventory to understand what personal data you gather, where it’s stored, and who has access to it. Include all touchpoints: checkout forms, contact pages, analytics tools, chatbots, etc.
• Have clear privacy policies. Ensure your privacy policy is transparent, accessible, and easy to understand. Outline what data is collected, why it’s needed, how it’s stored, and how users can opt-out or request deletion.
• Get explicit consent. Use cookie banners and opt-in checkboxes to collect informed, active consent, especially for marketing and tracking cookies.
• Offer data control to users. Give customers the ability to access, edit, or delete their data. Include instructions in your privacy policy or user dashboard.
• Secure the data you collect. All compliance efforts are moot without proper protection. Implement encryption, access controls, and breach response plans to back up your promises with action.

E-commerce Security Is Ongoing, Not One-and-Done

Security is never “done.” It’s a living, breathing part of your business that requires constant attention, smart tooling, and a proactive mindset. With threats evolving daily and customer expectations at an all-time high, protecting your online store is about more than just checking boxes; it’s about building trust and resilience in everything you do.

But we get it, security is complex, and not every business has the time, tools, or in-house expertise to manage it all. That’s where having a trusted partner can make all the difference.

At Svitla Systems, we’ve helped e-commerce brands of all sizes strengthen their digital storefronts, implement end-to-end security strategies, and stay ahead of compliance demands, without disrupting day-to-day operations. Whether you're looking to audit your existing setup, integrate secure technologies, or build a custom security roadmap, our experts are here to support you.

Not with templates. Not with guesswork. With real technical depth and a deep understanding of how e-commerce works.

If you're serious about protecting your customers, your data, and your brand, let’s talk. We’d love to help you build an online store that’s functional, fast, and also fortified against today’s most pressing cyber threats.