How to Test Shopify Store Security: Complete Guide (2025)

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Your Shopify store faces serious cyber threats every day. With data breaches costing an average of $4.88 million and retail ranking among the top targeted industries, security can’t be an afterthought. Bot attacks on online stores have nearly doubled, jumping from 26% to 43% between 2022 and 2023.

Shopify provides excellent security infrastructure, but it doesn’t cover everything.

You still need to secure what you control.

This guide shows you exactly how to test and protect your Shopify store in 2025. We’ll cover what Shopify already handles, what’s your responsibility, and most importantly, how to run proper security tests to find vulnerabilities before hackers do.

Whether you’re implementing direct checkout links, setting up analytics tracking, or managing discount campaigns, security must be foundational to your e-commerce strategy.

What Does Shopify Secure vs. What You Need to Protect?

Shopify operates as a SaaS platform, so they handle the heavy security lifting for core infrastructure. Every store automatically benefits from impressive built-in protections:

What Shopify Secures for You:

SSL encryption for all traffic

Every Shopify store includes SSL certificates for secure data transmission

PCI-DSS compliant checkout

Level 1 PCI compliance by default means you never handle raw credit card data

Network security and DDoS protection

Integrated threat management monitors and defends Shopify’s servers 24/7

The platform is solid. But here’s where it gets tricky.

Critical insight: While Shopify manages core platform security, merchants are responsible for specific elements involving customized code and integrations.

Your Security Responsibilities:

→ Staff accounts and passwords: You control who accesses your admin and how secure their credentials are

→ Third-party apps: Every app you install gets API permissions to your store data

→ Custom themes and code: Your Liquid templates and script tags can introduce vulnerabilities

→ External integrations: API keys and webhooks for CRMs, analytics, or custom checkout solutions

→ Operational security: Device security, phishing prevention, and suspicious activity monitoring

As one security expert explained on Shopify’s community forums: while Shopify runs tight security on their end, “the lion’s share” of a merchant’s security posture involves internal practices.

Think of it this way: Shopify provides a secure foundation, but you build the walls and lock the doors.

11 Shopify Security Best Practices to Prevent Cyber Attacks

Before diving into advanced testing, nail the basics. Most cyberattacks exploit simple weaknesses that proper security hygiene prevents.

1. Strengthen Account Security

Enable strong passwords and 2FA for ALL accounts. Use at least 12 characters with mixed types, plus enable two-factor authentication natively in Shopify. This blocks the vast majority of unauthorized access attempts.

Also use a reputable password manager instead of reusing credentials across accounts.

2. Apply Principle of Least Privilege

Give each staff account the minimum access needed for their specific job. A marketing intern doesn’t need full admin rights. Regularly audit user roles and remove accounts for former employees.

Why this matters: Even if one staff account gets compromised, the attacker’s access remains constrained.

3. Clean House Regularly

Remove unused apps and themes completely. Dormant apps often retain API access to your store, creating unnecessary risk. Old themes may contain undiscovered vulnerabilities.

Keep your Shopify environment lean. Every extra integration expands your attack surface. When you do need to add functionality, prioritize solutions like Checkout Links’ built-in features over multiple separate apps.

4. Stay Updated

Keep apps, themes, and integrations updated with the latest versions. Developers release updates to patch security issues and improve compatibility.

An outdated app could have known flaws that hackers actively exploit. Make it routine (monthly) to check for updates or enable auto-updates when possible.

5. Activate Built-In Security Features

Shopify provides several security tools out-of-the-box:

ReCAPTCHA Protection: Enable Google reCAPTCHA for contact forms and newsletter sign-ups in your Online Store preferences. With bot attacks nearly doubling, this protection is essential during sale periods. This is especially important if you’re using QR codes for marketing, as these can be targeted by bot scanners.

Checkout spam protection: Consider apps like Shop Protector for fake account creation or enable captcha challenges for suspicious checkout behavior.

Login attempt monitoring: Shopify automatically locks accounts after failed login attempts. Don’t disable this feature.

6. Use Trusted Payment Methods

Stick to Shopify Payments or approved gateways that are PCI compliant with built-in fraud checks. Avoid redirecting customers to obscure payment providers.

Never handle raw card data yourself on Shopify.

Enable 3D Secure when available for additional fraud protection and chargeback liability shift. Secure payment processing is especially critical when implementing direct checkout flows that bypass traditional cart pages.

7. Implement Fraud Prevention

Take advantage of Shopify’s fraud analysis indicators on orders (AVS mismatch, IP geolocation issues). For higher-risk transactions, set rules for manual review.

Consider services like Signifyd, NoFraud, or Shopify’s built-in Fraud Protect for guaranteed protection. Monitor order logs and admin logs for unusual activity. Advanced analytics help identify patterns in fraudulent behavior and track the security impact of different traffic sources.

8. Back Up Store Data

While Shopify is reliable, it doesn’t provide native full backups for all content. Use reputable backup apps like Rewind to automatically preserve products, customers, and themes. This includes backing up any custom discount configurations or promotional campaigns you’ve created.

Test your backups occasionally to ensure they’re valid.

9. Train Your Team

Human error causes many security breaches. Train staff to recognize phishing emails and fake login pages impersonating Shopify support.

Never share passwords or OTP codes via email or chat.

Establish an incident response plan so anyone suspecting a breach knows exactly how to alert you immediately. This is especially important for high-converting campaigns where security incidents could impact significant revenue.

10. Choose Apps Carefully

Stick to apps from reputable developers with good reviews and App Store history. Check for a “Built for Shopify” badge, indicating the app meets Shopify’s highest security and quality standards.

For example, Checkout Links is a Built for Shopify app, meaning it was vetted for secure coding, data handling, and performance. These apps undergo strict security reviews.

Always review the permissions an app requests during installation. If a discount app wants customer data access, that’s a red flag.

Security Check	What to Verify	Red Flags
App permissions	Minimum scopes needed	Excessive data requests
Developer reputation	Good reviews, long history	New developer, bad reviews
Built for Shopify badge	Present and verified	Missing badge
Update frequency	Regular updates	Abandoned apps

11. Secure Your Devices

Ensure computers used to access Shopify have updated operating systems, antivirus software, and firewalls. If you work on public Wi-Fi, use a VPN.

Treat your Shopify login like online banking. Avoid random or shared computers.

This is critical when managing time-sensitive promotions or limited-use links that could be compromised by unauthorized access.

How to Run Advanced Shopify Security Tests (Audits & Penetration Testing)

Once your basic security hygiene is solid, it’s time to test your defenses rigorously. This ranges from DIY audits to professional penetration tests.

Security testing in the Shopify context includes any activity verifying your store’s configurations, code, and integrations:

→ Vulnerability Scanning

Automated tools scan for known vulnerabilities or misconfigurations

→ Security Audit

Systematic review of settings, access controls, and compliance

→ Penetration Testing

Simulating cyberattacks to probe for weaknesses like a hacker would

Important distinction: You cannot pen-test Shopify’s core infrastructure (that violates terms of service). Instead, focus testing on custom code, third-party integrations, and configurations within your control.

How Often Should You Test?

Security testing isn’t one-and-done. Make it part of your maintenance schedule:

Quarterly (every 3 months): Light security audits, especially when adding apps or making theme changes. Review admin accounts, permissions, and run quick vulnerability scans. This includes testing any new marketing automation workflows or checkout optimization features.

Annually (or bi-annually): Comprehensive audits or penetration tests. Many experts suggest full security reviews every 6-12 months for high-volume stores.

After major changes or incidents: Run targeted tests after launching custom integrations, theme revamps, or news of new exploits.

5-Step Shopify Security Testing Framework (Complete Walkthrough)

Step 1: Planning and Scoping Your Test

Security testing needs a clear plan defining what you’ll test and how.

Identify High-Risk Areas

Think about which compromised areas would hurt most: customer data, order information, payment processing, and admin access. Set specific goals like “ensure unauthorized users can’t access customer order history” or “verify contact forms resist SQL injection.”

Focus on payment processing, customer data storage, API integrations, and admin access points. If you’re using advanced features like dynamic personalization or customer-specific links, these warrant extra testing attention.

Determine Scope and Boundaries

List components in-scope for testing:

① Your storefront web pages

② Theme code (Liquid, JavaScript, CSS)

③ Shopify admin configurations

④ Custom or private apps you’ve created

⑤ Third-party apps and their interfaces

⑥ Link sharing mechanisms and URL structures

List what’s out-of-scope (Shopify’s core checkout service, for example).

Get Approvals and Notify Parties

Secure written permission from stakeholders and establish a testing schedule. Set a testing window during low-traffic periods to avoid performance issues.

Have an emergency contact list ready if testing accidentally locks accounts or causes problems.

Choose Testing Tools

Common tools for web app security testing include:

Automated vulnerability scanners

OWASP ZAP, Nessus, Qualys for SQL injection, XSS, and misconfigurations

Browser developer tools and proxies

Chrome DevTools, Postman, Burp Suite to inspect network calls and test responses

Manual testing checklists

Using the OWASP Web Security Testing Guide

Configure tools carefully to avoid triggering Shopify’s rate limiting or performing accidental DoS attacks on your own store.

Step 2: Running Automated Scans

Start with automated scanning to catch obvious issues quickly.

Scan Your Storefront and Theme

Use web vulnerability scanners to crawl your site and test input fields for:

SQL injection vulnerabilities in search fields and forms

XSS (cross-site scripting) through forms or URL parameters

Insecure cookies or missing security headers

Other common web application flaws

Check SSL and Configuration

Use SSL checkers (like Qualys SSL Labs) to verify your certificate chain and TLS configuration. Shopify typically scores A+, but verify your custom domain is properly covered.

Focus Areas for Scanning:

Key areas to target with automated scans:

Scan Target	What to Check	Expected Result
Authentication	Login pages, admin interfaces	Proper session handling
Data Protection	Customer input endpoints	Input validation, encryption
Integrations	Third-party app scripts	No data exposure
Checkout/Payment	HTTPS coverage	No mixed content warnings
Admin Access	URL exposure, password policies	Secure admin controls

Interpret Scan Results

Your scanner will return potential vulnerabilities with risk ratings. Validate each finding since many are false positives.

Focus on high-risk findings: anything involving customer data leakage, authentication bypass, or malicious script execution capability.

Priority framework: Critical issues (actual SQL injection) should be fixed within 24 hours, High within 72 hours, Medium within a week, Low within two weeks.

Step 3: Manual Testing and Simulated Attacks

Automated scans catch breadth but miss logic issues.

Manual testing is where you think like a hacker.

Test Admin and Account Security

While you can’t penetrate Shopify’s admin directly, test your processes:

Verify 2FA is truly enabled for all staff accounts

Test password recovery processes for your admin accounts

Ensure departed staff accounts are promptly deactivated

Storefront Authentication Testing

If you use Shopify’s customer accounts:

Try reasonable brute force attempts to verify rate limiting

Ensure customers can’t view each other’s data by manipulating URLs

Test password reset tokens expire and can’t be reused

Forms and User Input Testing

Test every form with malicious payloads:

For SQL Injection: Try simple payloads like '; DROP TABLE users; -- or ' OR '1'='1 in form fields. Look for error messages mentioning SQL or databases.

For XSS: Input <script>alert('XSS')</script> in text fields. The script should be stripped or encoded, never executed.

For CSRF: Test custom forms to ensure they have proper CSRF tokens or session validation.

File Upload Testing: If your store allows file uploads through apps, test the mechanism. Ensure malicious files (like .php renamed as .jpg) don’t get executed.

Checkout Process Testing

Since Shopify’s core checkout is sealed:

If you’ve added checkout extensions or scripts, verify they don’t expose data or use untrusted sources

Test any custom payment integrations for logic flaws

For tools like Checkout Links that allow custom scripts, ensure you only add scripts you trust

Third-Party App Interaction Testing

Examine apps that add widgets or UI to your storefront:

Verify scripts load over HTTPS from correct sources

Use browser dev tools to check network requests

Test app widgets for input sanitization (like review submission forms)

Keep detailed notes of what you tried and results. Test both as logged-in users and anonymous visitors to check for privilege escalation or data leaks.

Step 4: Fixing Vulnerabilities

Triage findings by severity and address them systematically.

Priority Classification:

Severity	Response Time	Examples
Critical	24-hour fix	Direct customer data exposure, authentication bypass
High	72-hour fix	Stored XSS, privilege escalation, payment logic flaws
Medium	1-week fix	Missing security headers, input validation issues
Low	2-week fix	Information disclosure, minor configuration issues

Apply Fixes:

→ Configuration changes: Update settings, remove apps, adjust permissions

→ Code changes: Modify Liquid templates, update custom apps

→ App updates: Install patches from developers

→ Add security tools: Implement bot protection or fraud filtering

→ Remove functionality: Disable vulnerable features temporarily

Verify Fixes (Critical Step)

Re-run relevant tests to confirm vulnerabilities are resolved. Don’t consider issues closed until you’ve verified the fix works.

Document Everything

Create a security report recording:

Description of each problem

Severity and impact assessment

Steps to reproduce the issue

Fix applied and by whom

Date completed

This documentation helps with compliance, knowledge transfer, and future testing.

Step 5: Ongoing Monitoring and Improvement

Security is a continuous process requiring ongoing vigilance.

Set Up Monitoring:

Uptime and change monitoring for unexpected site modifications

Shopify security notifications (ensure owner email is monitored)

Consider security scanning services for continuous monitoring

Regular Maintenance:

Keep all software updated

Review new apps with zero trust until proven secure

Prefer “Built for Shopify” apps that meet strict safety criteria

For instance, Checkout Links being Built for Shopify means it demonstrated “safe, secure, and reliable” operation, including clean uninstallation and proper API usage.

Schedule Regular Audits

Make security reviews routine:

Monthly mini-audits: One hour reviewing security settings and logs

Quarterly reviews: Comprehensive settings and app permission audits

Annual penetration tests: Professional security assessments

Stay Informed

Follow the Shopify Changelog for security updates. Watch for major security news in retail that might apply to your setup.

With global cybercrime costs projected in the trillions, awareness is a powerful defense tool.

Best Shopify Security Tools and Features to Protect Your Store

Shopify’s ecosystem provides vetted solutions to strengthen security without building everything yourself.

Backup and Recovery

Consider apps like Rewind for automated backups or GitHub integration for theme version control. These protect against data loss and make incident recovery easier.

Security Monitoring

Apps can monitor theme changes, scan for malware, watch uptime, and notify you of suspicious activity. Use these as extra security layers.

Fraud Prevention

Beyond Shopify’s built-in fraud analysis, consider guarantee services like Signifyd or use Shopify Flow (Plus/Advanced plans) to automate responses to high-risk orders. Advanced conversion tracking helps distinguish legitimate high-value customers from potential fraud attempts.

Bot Protection

During major sales, use Shopify’s virtual queue system (Plus) or bot-blocking apps. Enable Google reCAPTCHA and consider services like Cloudflare for heavy bot traffic. Flash sale campaigns are particularly vulnerable to bot attacks due to their high-value, time-sensitive nature.

Shopify Plus Security Features

If you’re on Plus, use additional security tools:

Restrict checkout to specific domains

Use Shopify Scripts for cart logic checks

Implement Single Sign-On for admin access

Create separate private apps with minimal permissions

Use advanced A/B testing capabilities for security configurations

Built for Shopify Apps

Prioritize apps with the Built for Shopify badge. These undergo strict reviews for security, data usage, and performance.

Built for Shopify apps must demonstrate clean uninstallation, proper API usage, and secure data handling.

Checkout Links, for example, runs entirely on Shopify’s infrastructure and doesn’t inject code into your theme.

Using vetted integrations reduces your security burden while maintaining functionality.

Shopify Security Action Plan: Immediate Steps and Ongoing Tasks

Immediate Steps (This Week):

① Enable 2FA for all admin accounts

② Audit installed apps and remove unused ones

③ Update all apps and themes to latest versions

④ Enable Google reCAPTCHA on forms

⑤ Review staff permissions and apply least privilege

Monthly Tasks:

Check for app and theme updates

Review admin access logs for unusual activity

Verify backup systems are working

Scan for new security settings in Shopify admin

Quarterly Reviews:

→ Run automated vulnerability scans

→ Audit app permissions and access levels

→ Review and test incident response procedures

→ Check for new Built for Shopify alternatives to current apps

→ Test campaign attribution tracking for unusual patterns

Annual Security Audit:

Comprehensive penetration testing (professional or detailed DIY)

Full security policy review

Staff security training updates

Consider professional security assessment

How to Stay Protected Against Evolving E-commerce Cyber Threats

E-commerce cybercrime isn’t slowing down. Retail remains among the most targeted industries, with increasingly sophisticated attacks.

But by building on Shopify’s secure foundation and following systematic testing practices, you can stay ahead of most threats.

Remember the fundamentals:

Shopify provides excellent platform security, but you secure your customizations

Regular testing finds vulnerabilities before attackers do

Quick response to findings prevents small issues from becoming major breaches

Trusted partners and vetted apps reduce your security burden

A single breach can cost millions in damages and lost reputation, while solid security practices cost far less and actually add value. Customers buy more confidently when they trust their data is safe. This trust directly impacts conversion rates and customer lifetime value.

Your Shopify store’s security is an investment in business longevity. By making testing and monitoring routine habits, you’re protecting both your assets and your customers’ trust.

Stay vigilant, test regularly, and keep building on Shopify’s secure foundation. Whether you’re launching new email marketing campaigns, implementing cross-selling strategies, or optimizing your checkout flow, security should always be your foundation.

Your future self (and your customers) will thank you for the foresight.