Ecommerce Security Best Practices You Should Be Following

Security in ecommerce isn’t just a technical checkbox—it’s a trust signal. Customers are handing over payment details, home addresses, and personal preferences every time they complete a transaction. If they don’t feel safe, they won’t come back. A single breach can erode brand equity faster than any shipping delay or poor review.

That’s why ecommerce security needs to be embedded in every layer of your operation—from checkout logic to third-party integrations. For brands aiming to grow, security must scale in parallel. The tools and safeguards that worked at launch won’t cut it during peak season or international expansion. Here’s how to build security into your ecommerce foundation without sacrificing speed or customer experience.

Common Ecommerce Security Vulnerabilities

Cyber threats evolve as quickly as ecommerce platforms do. Many attacks are now automated, making even small or mid-sized brands targets. Understanding where vulnerabilities typically arise is the first step toward preventing them.

Payment Fraud

Card testing attacks, chargeback fraud, and account takeovers are among the most common threats to ecommerce sites. Bots often test thousands of stolen card numbers against checkout flows, looking for sites with weak fraud filters. Once a card works, it’s used for high-ticket purchases or resold.

Other tactics include:

• Fake accounts to exploit discount codes
• Use of stolen identities for high-value orders
• Refund fraud through false claims of nondelivery

API Exploits

APIs are essential to modern ecommerce, but they’re also an attack vector if not properly managed. Custom integrations—especially with CRMs, payment gateways, or ERPs—open potential gaps. Poor authentication, exposed endpoints, or outdated libraries can allow attackers to extract customer or order data and even inject malicious code into your frontend. 

Phishing and Credential Theft

Not all attacks are technical. Many breaches start with a simple phishing email. Employees might click links that mimic admin dashboards or vendor portals, unintentionally giving access to sensitive systems. Targeted phishing can also come through fake customer service requests or impersonated emails from logistics partners, which are hard to spot without proper training and systems in place.

Must-Have Ecommerce Security Protocols

Ecommerce brands can’t eliminate every risk, but they can make attacks much harder and less likely to succeed. These security protocols are non-negotiable.

Two-Factor Authentication (2FA)

Every admin and operations account should require 2FA—no exceptions. SMS-based verification is better than nothing, but app-based solutions (e.g., Google Authenticator, Authy) or hardware tokens offer stronger protection.

Best practices include:

• Requiring 2FA for all staff with backend access
• Enforcing 2FA on connected platforms like Shopify, BigCommerce, or NetSuite
• Disabling access after multiple failed attempts or inactivity

PCI Compliance

If you accept credit cards, you’re responsible for PCI DSS (Payment Card Industry Data Security Standard) compliance—even if you use a third-party gateway.

At a minimum, this means:

• Not storing full credit card numbers
• Encrypting all transaction data in transit and at rest
• Running quarterly vulnerability scans
• Maintaining an incident response plan

Using PCI-compliant platforms helps, but you still need internal protocols that align with those standards.

Data Encryption

Customer data—including emails, addresses, and purchase history—should be encrypted both in transit and at rest. That means using HTTPS with strong TLS certificates for all pages, encrypting data stored in your CMS, CRM, or analytics tools, and regularly rotating encryption keys and credentials.

Never store sensitive customer information (like passwords or payment info) in plain text.

Regular Ecommerce Security Audits

Security isn’t something you review once a year. Regular audits ensure your defenses scale with your operations—and that you’re not vulnerable to overlooked gaps.

What Should Be Included

A thorough security audit should review platform and plugin vulnerabilities, admin user permissions and access logs, payment system configurations and fraud filters, third-party app integrations, server security and CDN settings, and API endpoint exposure and authentication.

Review customer data storage and handling protocols and also test how your system responds to simulated attacks (e.g., penetration testing or red team exercises).

How to Implement Ecommerce Security Best Practices Without Disruption

Ecommerce security best practices don’t have to bring operations to a halt. Most scanning and review processes can run in the background or during off-hours.

To keep them low-friction:

• Schedule audits quarterly or around major launches
• Maintain clear documentation of fixes and updates
• Use staging environments to test changes
• Work with external experts for unbiased reviews

Security doesn’t need to slow down growth—if anything, it helps prevent the setbacks that slow you down later.

3PL and Tech Partner Due Diligence

Even the most secure ecommerce brand is only as strong as its weakest partner. That’s why vetting 3PLs, payment providers, and tech vendors is essential. Your 3PL sees your orders, customer details, and product inventory. If they’re not following modern security protocols, you’re taking on unnecessary risk.

A reliable partner should:

• Use secure portals with role-based permissions
• Maintain SOC 2 or ISO 27001 certifications
• Support encrypted data transfers via API or EDI
• Limit physical access to fulfillment zones

Shipfusion, for example, adheres to strict security practices and builds proprietary tools that allow full control over inventory visibility without exposing customer data. On the tech side, review each vendor’s security posture: Are they GDPR and CCPA compliant? Do they offer 2FA and access logs? How often do they update and patch vulnerabilities? What’s their incident response plan? Ask these questions during onboarding, not after a breach.

Shipfusion Embraces Ecommerce Security Best Practices In Full

The moment customers doubt your ability to protect their information, they hesitate to buy, return orders less often, and warn others away. That’s why ecommerce security best practices should be non-negotiable for every growing brand.

Now’s the time to conduct a full security check. Review platform and plugin updates, lock down access permissions, and enforce 2FA. Scan for exposed endpoints and outdated integrations, and remember to ask fulfillment and tech partners for documentation of their security protocols.

As your store grows, your exposure does too. Don’t wait for a breach to find the cracks. Take a proactive stance on ecommerce security, and reinforce the trust that drives your business forward.

Want a fulfillment partner that won’t compromise your data security? Shipfusion’s proprietary platform is built with privacy and compliance at the forefront.

Request a free consultation to see how we help growing brands stay secure as they scale.