Shopify Security Checklist for Ecommerce Stores

Staff Roles and Account Management

Shopify's staff account system allows you to grant different levels of access to team members, contractors, and agencies. Using this system properly is the single most important security measure within your control.

Create individual staff accounts for each person who needs access to your Shopify admin. Never share your store owner account credentials. The store owner account has unrestricted access to everything — including financial data, billing, and the ability to close the store. This account should be protected with the strongest possible password and 2FA, and used only when owner-level permissions are genuinely required.

Assign permissions based on what each person actually needs to do. Your customer service representative needs access to orders and customer information but not to themes, apps, or store settings. Your marketing person needs access to discounts and marketing tools but not to financial reports or staff management. Shopify allows granular permission control — use it.

Review your staff list monthly. Remove accounts for anyone who no longer works with your business. This includes seasonal employees, contractors whose projects have ended, and agencies you no longer work with. Active credentials for former team members are a preventable security risk.

Enable two-factor authentication as a requirement for all staff accounts. Shopify supports 2FA at the staff level, and there is no legitimate reason not to require it. A single compromised staff account can lead to data exposure, fraudulent orders, or unauthorised store modifications.

Admin Access Hygiene

Beyond staff accounts, your admin access hygiene encompasses how you interact with your Shopify dashboard day-to-day and how you manage the credentials that protect your store.

Use a unique, strong password for your Shopify store owner account. This password should not be used anywhere else — not for your personal email, not for your other business accounts, nowhere. Use a password manager to generate and store a random password of at least 20 characters.

Be cautious about where and how you access your Shopify admin. Avoid logging in from public Wi-Fi networks, shared computers, or devices you do not control. If you need to manage your store while travelling, use a VPN to encrypt your connection.

Monitor your login history regularly. Shopify records login activity including IP addresses and device information. If you see logins from locations or devices you do not recognise, change your password immediately and review your staff accounts for unauthorised additions.

Keep your registered email address secure. Your Shopify account recovery process relies on your registered email. If that email account is compromised, an attacker could potentially reset your Shopify password and gain full access to your store. Protect your email account with a strong, unique password and 2FA.

App Permissions and Third-Party Integrations

Shopify apps extend your store's functionality, but every app you install is granted access to some of your store's data. Understanding and managing app permissions is a critical security responsibility.

Before installing any app, review the permissions it requests. Shopify displays these during installation. Does a simple countdown timer really need access to your customer data? Does a currency converter need access to your orders? If the permissions seem excessive for the app's stated purpose, look for alternatives with a smaller permission footprint.

Audit your installed apps quarterly. Remove any apps you are no longer using. Even if an app is just sitting idle in your store, it retains whatever data access permissions it was granted during installation. Fewer apps means fewer potential access points and a smaller risk surface.

Pay attention to app reviews and update history. Apps that have not been updated in over six months, have numerous negative reviews mentioning bugs or security issues, or are developed by unknown entities carry higher risk. The Shopify App Store review process catches some issues, but not all.

When an app is removed, it should lose access to your store data. However, data that was already exported or cached by the app's servers remains with the app developer. Choose apps from reputable developers with clear privacy policies, especially for apps that handle customer data, payment information, or order history.

Fraud and Chargeback Management

Fraud protection is a merchant responsibility that falls outside Shopify's platform security scope. While Shopify provides built-in fraud analysis indicators on orders, interpreting those signals and making fulfilment decisions is up to you.

Understand Shopify's fraud analysis. Every order receives a risk indicator based on factors like IP location, billing/shipping address match, card type, and order history. High-risk indicators are not automatic fraud — they are signals that warrant further review before fulfilment. Develop a process for manually reviewing orders that trigger high-risk warnings.

Implement address verification and card verification (CVV) for all transactions. These basic checks filter out a significant portion of fraudulent payment attempts. Shopify's payment settings allow you to require these verifications — ensure they are enabled.

For high-value orders, consider adding manual review steps. A phone call or email verification for orders above a certain threshold can prevent the most damaging instances of fraud. The small operational overhead is justified by the chargeback costs it prevents — each chargeback typically costs AED 50-100 in fees alone, on top of the lost merchandise.

Keep detailed records of all transactions, shipping confirmations, and customer communications. In the event of a chargeback dispute, documentation is your primary defence. Shopify provides transaction records, but supplementary evidence like delivery confirmation photos and signed receipts strengthens your case significantly.

What Shopify Handles vs What You Must Handle

Understanding the division of responsibility is essential for knowing where to focus your security efforts. Shopify handles a substantial portion of the security stack — but not all of it.

Shopify is responsible for: server infrastructure security, SSL certificate management, PCI-DSS Level 1 compliance, platform DDoS protection, automatic platform updates and patches, payment processing security (through Shopify Payments), and physical data centre security.

You are responsible for: store owner and staff account security, app installation decisions and permission management, fraud detection and order review, customer data handling and privacy compliance, storefront content security (preventing injection through custom code), marketing email security and phishing awareness, and third-party integration credential management.

This division means that as a Shopify store owner, your security focus should be on access management, app hygiene, and business process security — not on server hardening or infrastructure patching. Directing your limited time and resources to the areas you actually control is far more effective than worrying about aspects Shopify already manages.

What This Means for Your Business

Shopify provides an excellent security foundation — far better than what most small ecommerce businesses could build independently. But the platform cannot protect you from weak passwords, excessive app permissions, or poor fraud management. Those are your domain.

The security measures in this checklist are straightforward and manageable for any store owner. They do not require technical expertise. What they require is consistency — monthly reviews, prompt removal of old accounts, and disciplined app management.

If you run a growing ecommerce operation and want professional oversight of your store's security posture, managed security services can handle the ongoing monitoring, staff access reviews, and app security audits. This is especially valuable for stores with multiple staff members, high transaction volumes, or plans to scale.

When This Checklist Needs Expansion

Shopify Plus merchants have additional security options (custom checkout, API access, dedicated support) that create both opportunities and additional responsibilities. This checklist covers standard Shopify plans — Plus merchants should work with their Shopify Plus partner for expanded security guidance.

Stores with custom themes or significant custom Liquid code have additional security considerations around code injection and cross-site scripting. If your storefront includes custom JavaScript, ensure it is reviewed by a developer familiar with ecommerce security.

International stores operating across multiple regulatory jurisdictions may need additional compliance measures beyond what this checklist covers, including GDPR, CCPA, and UAE-specific data protection requirements.