How to Secure Your Ecommerce Store: A 10-Point Checklist

What happens when your ecommerce store’s security is compromised?

The fallout can be catastrophic.

Lost sales, a damaged reputation, and customers who may never return.

In fact, the IBM Security Cost of a Data Breach Report shows that the average cost of a data breach is $4.88 million! This includes legal costs, customer churn, and long-term reputation damage.

Quick Answer: How to secure your ecommerce store

Secure your ecommerce store by choosing a secure host, installing SSL certificates, using PCI-compliant payment gateways, enforcing strong login procedures, deploying a web application firewall, updating all software, scheduling malware scans, controlling user access, automating backups, and educating your team on cybersecurity best practices.

But here’s the good news: you can protect your store before disaster strikes.

In this guide, you’ll learn how hackers can target your ecommerce store and, more importantly, how you can prevent them.

Disclaimer: This article is for informational purposes only and does not constitute legal or cybersecurity advice. Always consult a cybersecurity expert or your ecommerce platform’s support team to ensure your store meets security and compliance requirements.

Why does your ecommerce store need more security?

When customers shop at your store, they trust you with their personal and financial information, such as credit card details, addresses, and contact information.

They expect it to be safe and secure.

Yet many online stores still lack modern security measures, leaving them open to increasingly sophisticated cyberattacks. 

Here’s what’s at stake:

• Financial loss. Security breaches can cost a fortune. Fraud, chargebacks, and the expenses of fixing a breach all add up fast. 
• Customer confidence. Shoppers look for security signals like 'https://' and the padlock icon in their browser. If your checkout process appears insecure, customers may abandon their carts. In fact, studies show that up to 70% of consumers will leave a site if they doubt its security. 
• Performance. Cyberattacks like DDoS attacks can shut your website down, leading to lost sales and frustrated customers.
• Changing threats. Hackers constantly develop new tactics to break into stores, such as phishing emails, malware, and ransomware.
• Internal and partner risks. Many breaches happen because of weak internal practices, such as employees using simple, repeated passwords or third-party apps that haven’t been properly secured.
• Legal issues. Regulations like GDPR and the California Consumer Privacy Act (CCPA) require businesses to follow strict security protocols, like using SSL certificates and PCI DSS compliance. Failing to meet these standards can lead to fines, legal headaches, and a damaged reputation.

What are the biggest security risks facing your ecommerce website?

Protecting your online store starts with understanding where the weak spots are. 

Here are the seven biggest threats you need to be aware of:

1. Malware

Malware is malicious software that sneaks into your system through infected files, downloads, or dodgy links.

For example, an employee might open what looks like a regular invoice, only to trigger ransomware that locks down your entire store until you pay a ransom.

Other common types of malware include:

• Trojans. Fake software pretending to be legit but actually steals data in the background.
• Scareware. Alarming pop-ups claiming your device is infected, tricking you into downloading fake antivirus software.
• Adware. Pop-ups or uncloseable windows that hijack your website and flood it with ads.
• Rootkits. Hidden malware that gives hackers deep access to your system without detection.

2. Unauthorized account access

Hackers love weak passwords as they give them easy entry to customer and admin accounts.

Just an employee using the same simple password for multiple sites is enough for them. You can protect yourself by:

• Enforcing strong, unique passwords with a tool like 1Password.
• Enabling two-factor authentication (2FA) to add an extra security layer.
• Limiting admin access to only those who need it.

3. SQL injection

SQL injections (Structured Query Language) is a coding language to access databases.

Cybercriminals insert malicious SQL code into input fields such as login or search boxes to trick your database into revealing sensitive information. 

For example, a hacker might insert harmful code in a product review, which, when viewed, steals session cookies or redirects users to a fake site.

4. Cross-site scripting

Hackers use XSS attacks to inject malicious scripts into user-generated content like product reviews or comments.

Basically, they turn your site into a weapon against your own customers.

This type of attack is especially effective on platforms that allow public interactions, like forums, message boards, or product pages.

Additionally, an XSS attack may alter your website. Your content may be changed or even disappear entirely by redirecting all traffic to another site.

5. E-skimming

E-skimming, sometimes called Magecart attacks, targets your checkout process. 

Hackers inject hidden code into your payment page to steal customer credit card details in real-time. They then sell this data on the dark web.

6. DDoS

A Distributed Denial of Service (DDoS) attack floods your store with massive amounts of fake traffic, causing crashes during peak shopping times like Black Friday. 

Think of it as a traffic jam that blocks real customers from reaching your store.

Using a Web Application Firewall (WAF) and a Content Delivery Network (CDN) like Cloudflare helps filter out this bogus traffic and keep your store online.

7. Brute force

Hackers use automated bots to repeatedly guess login credentials until they crack them.

This method, called password spraying, is one of the simplest yet most effective hacking methods.

The best way to protect your store from brute force attacks is to enable captcha challenges, use two-factor authentication, and complex passwords.

10 ways to secure your ecommerce store

Now that you know the most common security threats, it’s time to take action.

Here’s a practical security checklist to help you safeguard your ecommerce business:

1. Pick a secure host and platform

Your ecommerce platform and web host are your store’s first line of defense against cyber threats. The right choice can help protect your business from hacks, fraud, and downtime, while the wrong one leaves you vulnerable.

However, not all ecommerce platforms offer the same level of security. 

Some platforms, like Shopify and BigCommerce, handle security on their end, while others, like WooCommerce, require you to manage it yourself.

For example, Shopify is a fully hosted ecommerce solution, meaning security patches, PCI compliance, and server protections are all taken care of for you.

In fact, Shopify also has built-in fraud analysis tools that help detect high-risk transactions before they become a problem.

WooCommerce, on the other hand, is a self-hosted solution that runs on WordPress. This means you are responsible for securing your store:

You’ll need to choose a secure hosting provider, install SSL certificates, set up firewalls, and regularly update WordPress, WooCommerce, and all plugins to prevent vulnerabilities. 

If you’re using WooCommerce, we recommend using either Kinsta or SiteGround for easy, hassle-free management, or Cloudways if you have some technical expertise and want more control over your server setup

Note: Not sure which ecommerce platform is right for you? Take our ecommerce platform quiz to get a personalized recommendation based on your needs. Or, try our Ecommerce Platform Advisor GPT to quickly find the best fit for your store!

2. Install an SSL certificate and switch to HTTPS

SSL (Secure Sockets Layer) encrypts the connection between your website and your customers, which ensures that all data remains private and protected.

When an SSL certificate is installed, your website URL changes from HTTP to HTTPS, and a padlock icon appears in the browser bar — an instant trust signal for shoppers.

If your store doesn’t have SSL, browsers will flag it as 'Not Secure,' which can scare customers away before they even make a purchase.

Google also favors HTTPS-secured websites in search rankings, so an unsecured site could hurt both your traffic and sales.

Most ecommerce platforms, like Shopify and BigCommerce, provide free SSL certificates automatically, so you don’t have to worry about setting it up.

If you’re using WooCommerce or another self-hosted platform, you’ll need to install SSL manually through your hosting provider.

3. Secure payment processing and become PCI-compliant

The most secure way to process payments is to never store credit card details on your server.

Instead, use trusted payment processors like Stripe, PayPal, or Authorize.Net, which handle transactions securely and protect sensitive data through:

• Encrypted checkout tunnels. Customer payment details go directly to the bank, never touching your website.
• Tokenization. Sensitive card details are replaced with a randomized code, making them useless if intercepted.

To further reduce fraud, you should:

• Enable fraud prevention settings in your payment processor’s dashboard.
• Require AVS (Address Verification System) and CVV checks to reduce chargebacks.
• Monitor transactions for red flags like large first-time orders or multiple failed payment attempts.

And, to ensure full security compliance, your store must follow PCI DSS (Payment Card Industry Data Security Standard). 

If you’re using Shopify, BigCommerce, or another hosted platform, PCI compliance is handled for you.

However, if you’re on WooCommerce or Magento, you’ll need to ensure compliance yourself by using a PCI-compliant payment gateway and maintaining security best practices.

4. Enforce secure login procedures

Your store’s login page is the front door to your business — if it’s not secure, hackers can force their way in.

To stop this:

• Enable multi-factor authentication (MFA). Even if a password is stolen, a second verification step (like a one-time code) is needed.
• Limit failed login attempts. This blocks brute-force attacks, where hackers try endless password combinations.
• Use a password manager. Tools like 1Password to create and store strong, unique passwords.
• Consider burner emails for non-essential accounts. If login credentials get exposed, your primary email stays safe.

5. Add fraud detection and monitor activity logs

Fraudsters are always coming up with new ways to scam businesses. 

To stay ahead, you need real-time fraud detection tools and active store monitoring.

Most hosted ecommerce platforms, like Shopify, offer built-in fraud analysis that flags risky orders based on billing-shipping mismatches, unusual IP addresses, or suspicious payment activity.

This tool is good enough for small to medium-sized businesses. But if it marks an order as high risk and you’re unsure, just call the customer before processing it.

Fraudsters tend to avoid calls or act defensively if questioned.

For self-hosted platforms like WooCommerce, fraud prevention isn’t built in. 

Instead, you can add security layers like:

• A firewall (Cloudflare) to block bad traffic.
• Fraud detection settings in your payment processor’s dashboard.

If you operate in a high-fraud ecommerce category (e.g., electronics, luxury goods, gift cards), adding an extra layer of protection with fraud detection tools like Signifyd or SEON can help.

These tools analyze IP addresses, email history, device fingerprinting, and transaction behavior to identify fraud patterns. 

For example, if a scammer places multiple orders using different credit cards from the same device or if the billing and shipping addresses don’t match, these tools automatically flag or block the transaction.

Besides automated detection, you should manually monitor your ecommerce store. Keep an eye on your activity logs for:

• Frequent changes to shipping addresses (possible account takeover).
• Repeated failed login attempts from different locations (hacking attempts).
• Large orders from a first-time customer with express shipping (stolen card alert!).

6. Deploy a web application firewall (WAF)

A Web Application Firewall (WAF) acts as a security guard which blocks suspicious activity before it can cause damage.

Imagine running a flash sale, and suddenly your store slows down or crashes because of a DDoS attack — a flood of fake traffic meant to overwhelm your site.

Or worse, a hacker sneaks in malicious code to steal customer logins.

A WAF detects and blocks these threats, ensuring only legitimate visitors can access your store.

If you’re using Shopify, security protections are built in, but if you’re on WooCommerce or Magento, you’ll need to set up a third-party WAF like Cloudflare, Sucuri, WordFence, or AWS WAF.

7. Update your platform, themes, and plugins

Hackers actively target old versions of platforms, themes, and plugins to exploit vulnerabilities.

If you’re on Shopify or BigCommerce, you don’t have to worry as updates happen automatically.

But if you use WooCommerce, Magento, or another self-hosted platform, it’s on you to keep everything up to date.

Unused or outdated plugins can be major security risks, so delete anything you no longer use.

Before installing new plugins, check reviews, developer responses, and update frequency to ensure it’s well-maintained. 

Where possible, enable automatic updates to keep your store secure without extra work.

8. Schedule regular malware scans

Automated malware scans run in the background, constantly checking your store for hidden threats like malicious code, spam injections, and checkout hijacking.

If you run a WooCommerce store, you can start with a free Wordfence plan alongside a firewall (as covered earlier) and a managed WordPress host like Kinsta.

As your store grows, you can look into paid tools like Sucuri, Malwarebytes, BeagleSecurity, or GetAstra for deeper protection.

Most security tools monitor your site 24/7 and block requests from a wide range of threats, including malware, ransomware, and phishing attacks.

9. Control user access

Not everyone on your team needs full access to your ecommerce store.

Giving too much access can lead to accidental mistakes, security risks, or even fraud.

So only give people the access they actually need—nothing more.

On Shopify, you can set up staff roles with different permissions so employees can only access what’s relevant to their job — whether it’s managing orders, editing products, or handling refunds.

On WooCommerce, be mindful of roles like Shop Manager, which allows users to process orders and refunds. Keep admin access limited to one or two trusted people.

If someone only needs to add blog posts or update product descriptions, assign them Editor, Author, or Contributor roles instead.

For extra security on WooCommerce, hiding or changing your default login URL makes it harder for hackers to find your login page.

Tip: Check out these step-by-step guides for WordPress and Shopify to ensure your data stays safe.

10. Schedule automated backups

Imagine waking up to find your entire store has crashed: whether due to a cyberattack, a technical glitch, or even an accidental deletion. 

Without a backup, you’re starting from scratch.

That’s why automated backups are a lifesaver. They ensure you always have a restorable version of your store in case something goes wrong.

Luckily, Shopify automatically backs up your store, but restoring data requires contacting support. To stay in control, use apps like Rewind Backups.

On WooCommerce, you’ll need to set up backups manually. Managed hosting providers like Kinsta, SiteGround, or WP Engine offer daily backups, while plugins like UpdraftPlus or Jetpack don't.

How do you protect your ecommerce store internally?

Not all security threats come from hackers — some come from within.

Here’s how to protect your store from internal risks:

• Access. Apply the principle of least privilege so employees only access what they need. Regularly review who has access to orders, payment details, and customer information and remove unnecessary permissions.
• Monitor. Keep track of who is making changes to products, orders, and store settings. All ecommerce platforms provide activity logs where you can check for suspicious edits.
• Educate. Mistakes like clicking on phishing emails can expose your store to malware or data breaches. So, train employees to recognize scam emails, fake invoices, and suspicious links.
• Deactivate. If an employee or contractor leaves, their access should be revoked immediately to prevent potential sabotage or data theft.
• Schedule. Set a routine to review access logs, staff accounts, and permissions. Remove inactive users and tighten security settings if needed.

How do you future-proof your ecommerce security strategy?

What worked yesterday might not be enough tomorrow.

Instead of just reacting to threats, stay ahead and build a security strategy that keeps your store safe in the long run.

Here’s how you can do that:

• Use a CDN. A Content Delivery Network (CDN) like Cloudflare or Akamai speeds up your store while blocking DDoS attacks, preventing downtime caused by fake traffic floods.
• Have a plan. Even with strong security, things can go wrong. Have a clear plan for handling breaches, including who to contact, how to restore backups, and how to notify affected customers.
• Cyber insurance. A major data breach or fraud attack can mean massive losses: legal fees, fines, and even customer lawsuits. Cyber insurance helps cover financial damages, liability claims, and PR crisis management if your store is hit.
• Get an expert. If your store is scaling fast, consider hiring a cybersecurity specialist to audit your site, test for vulnerabilities, and patch weak spots before hackers exploit them. This is especially important for high-value transactions, sensitive customer data, or industries like electronics and luxury goods.
• Explore platform-specific security guides. Every ecommerce platform has its own security best practices. Shopify, WooCommerce, and Magento all offer security recommendations tailored to their systems. 
• Use a VPN (Virtual Private Network). A VPN encrypts your connection, keeping your store’s sensitive data safe, especially when managing your business on public Wi-Fi. It also lets you geo-test your store, checking regional pricing and competitor stores without exposing your real IP address.

Summary

Before we go, we've created a quick summary of this article for you, so you can easily remember it:

• Shopify handles security for you, while WooCommerce requires manual setup of SSL, firewalls, and regular updates to minimize vulnerability.
• Use PCI-compliant payment gateways like Stripe or PayPal, which implement encryption protocols to safeguard transactions. Enable AVS and CVV checks, and monitor for suspicious activity to reduce fraud threats.
• Strong passwords, multi-factor authentication (MFA), and limited staff permissions help prevent unauthorized access. Regularly review who has access to what.
• Use Web Application Firewalls (WAF) like Cloudflare to block cyber threats, and run automated malware scans with tools like Sucuri, Jetpack Scan, or Bitdefender to catch infections early.
• Outdated plugins and themes are easy targets for hackers. To restore your store quickly if something goes wrong, regularly update your site and schedule automatic backups with UpdraftPlus for WooCommerce or Rewind for Shopify.
• Limit staff access, monitor admin activity logs, and train your team to spot phishing scams so mistakes or insider threats don’t put your store at risk.
• Use a VPN for secure browsing and geo-testing, integrate a CDN to prevent DDoS attacks, and stay informed on new security threats to keep your store protected in the future.

Final thoughts

We know you already have a million things to manage — orders, marketing, customer service — and adding security to the mix can feel overwhelming.

But taking small, consistent steps today can save you from major headaches and financial losses down the road.

Your hard work deserves protection. That is why you must stay safe and prepare for the long run.

Hopefully, this guide has helped you feel more confident about securing your store! 🙂

Want to learn more about ecommerce?

Ready to move your online store to the next level? Check out the articles below:

• How to Check if a Product Is Trademarked or Copyrighted
• What Is Shopify’s Shop Channel? (And How Do You Use It?)
• 10 Best Ecommerce Automation Tools for Your Store in 2025

Plus, don't forget to check out our in-depth how to start an online store guide here.