The Biggest Security Mistakes eCommerce Stores Make

The average ecommerce data breach now costs $3.54 million — and 80% of retailers faced at least one cyberattack in 2025. The stores that survive aren’t the ones with the biggest budgets. They’re the ones that closed the obvious gaps first.

Ecommerce stores are complex ecosystems. Product pages, checkout flows, customer accounts, inventory systems, payment processors, loyalty programs, and dozens of third-party apps — all connected, all running simultaneously, and all representing potential entry points for attackers. That complexity is exactly what criminals count on.

According to the Verizon 2025 Data Breach Investigations Report, the retail sector experienced 837 cyber incidents leading to 419 confirmed data breaches in 2025 alone. Retail cyber attacks increased 34% year over year, and IBM’s 2025 Cost of a Data Breach Report puts the average retail breach cost at $3.54 million. For US-based businesses, that number climbs to $10.22 million — an all-time high.

The good news: most of these breaches are preventable. The mistakes that let attackers in are well-documented, consistent, and fixable. Below is a no-fluff breakdown of the biggest security errors ecommerce stores make in 2025 — and the practical steps to close each gap before it costs you.

1. Weak or Single-Factor Authentication

Passwords are breached, stolen, guessed, and sold in bulk on dark web marketplaces. Short, reused, or shared admin passwords give attackers a direct path into your store’s backend. This is not a theoretical risk: compromised credentials were linked to 55% of retail breaches in 2025, according to PureCyber, and authentication failures remain one of the most common initial access methods across all industries.

The fix is both straightforward and non-negotiable. Require multi-factor authentication (MFA) for every admin account, every staff login, and every third-party platform that touches your store. On Shopify, you can enforce organization-level two-factor authentication across all staff accounts and integrate directly with enterprise identity providers like Okta, Azure, and OneLogin via SAML and SCIM. For higher-security environments, FIDO2 passkeys eliminate the password entirely.

Operationally: force long, unique passwords stored in a vault (1Password, Bitwarden, or equivalent), train every team member to use a password manager, and rotate all credentials immediately after any personnel change — including contractors, agency partners, and seasonal staff. One departed employee with lingering admin access is all it takes.

2. Unpatched Platforms, Themes, and Plugins

Unpatched web applications are among the most reliable “way in” for attackers. Vulnerability exploitation as an initial access vector grew 34% year over year in 2024, accounting for 20% of all confirmed breaches. Attackers don’t manually probe sites — they run automated scanners that identify known CVEs across thousands of domains simultaneously. If your platform, theme, or plugin has a known vulnerability and you haven’t patched it, you’re already on a list.

The discipline required here is simple but often skipped: schedule regular maintenance windows, apply security updates to your store platform and all extensions promptly, and always test updates on a staging environment before deploying to production. If you genuinely cannot patch immediately, isolate or temporarily disable the vulnerable component rather than leaving it exposed. For Shopify merchants, the platform handles core infrastructure patching — but theme code, custom apps, and third-party integrations remain your responsibility.

3. Over-Reliance on Third-Party Services Without Monitoring

Payment gateways, analytics scripts, review widgets, chat tools, recommendation engines, loyalty apps — these integrations make modern ecommerce work. They also dramatically expand your attack surface. In 2025, approximately 30% of all data breaches were linked to third-party entities, nearly double the 15% rate recorded in 2024. A compromised vendor can inject payment skimmers, exfiltrate customer PII, or silently redirect checkout traffic — and you may not know for weeks. The median breach discovery time in 2025 was 51 days.

Start with a complete inventory of every third-party integration your store uses. For each one, ask: what data can this vendor access? What happens if they’re breached? Limit the data each vendor can reach using the principle of least privilege. Implement Content Security Policy (CSP) headers and Subresource Integrity (SRI) checks where your platform supports them. Require written security commitments and SLAs from critical vendors, particularly those touching payment or customer data. And set up monitoring — if a vendor suffers a breach, your alerting should catch anomalous behavior before it compounds.

4. Exposed Remote Admin Panels and Insufficient Network Protections

Remote admin panels, SSH access, and store backend URLs left open to the public internet are standing invitations for brute-force attacks and credential stuffing. Attackers use automated tools to probe these endpoints continuously. The fix is layered: use VPNs or zero-trust access solutions for all sensitive remote connections, apply IP allow-listing to restrict admin panel access to known addresses, and use jump hosts for privileged infrastructure access.

For distributed or remote teams, require employees to connect through a corporate VPN before accessing store admin environments. For discrete admin connections and securing remote sessions, a reliable VPN solution like VeePN for services can serve as part of a layered approach — with minimal investment, it mitigates most attacks targeting data and devices in transit, regardless of office location. Combine this with zero-trust principles: never assume a connection is safe because it looks familiar. Verify every access attempt, every time.

5. No Centralized Logging or Monitoring

If an attacker is inside your store’s environment and you don’t know it, every hour they remain undetected compounds the damage. Too many ecommerce operators have no centralized logging, no alerting, and no regular review process. The result: attackers dwell for weeks or months before discovery, exfiltrating customer data, installing skimmers, or staging ransomware.

Deploy centralized logging — either a managed SIEM solution or a lightweight logging stack — and configure alerts for the events that matter most: unusual admin logins, new payment endpoints being added, sudden spikes in failed authentication, file changes in sensitive directories, and privilege escalation attempts. Even basic alerting rules on these five event types will dramatically reduce your mean time to detection. Retain logs for at least 90 days to support incident investigation. For Shopify Plus merchants, Shopify’s audit log provides a chronological record of staff actions and admin events — use it.

6. Excessive Privileges and Stale Access

Employees change roles. Contractors wrap projects. Agencies rotate account managers. Yet in most ecommerce operations, accounts accumulate permissions over time and are rarely reviewed. This creates a growing pool of over-privileged accounts — each one a potential entry point if credentials are ever compromised.

Enforce the principle of least privilege: every user gets only the access they need to do their current job, nothing more. Implement role-based access control (RBAC) and conduct a formal access review at least quarterly. Remove accounts belonging to departed staff on their last day — not eventually. Require MFA for all privileged roles. On Shopify, staff permissions are granular — use them. A customer service rep doesn’t need access to payment settings. A fulfillment partner doesn’t need access to marketing campaigns.

7. Phishing, Social Engineering, and Human Error

The human element remains the most consistently exploited attack vector in retail. According to PureCyber, 65% of retail breaches in 2025 included a phishing element, and a large share of all breaches involve some form of human error — misdirected invoices, accidental data exposure, or employees clicking malicious links. Attackers don’t need to break through your firewall if they can convince a team member to hand over credentials voluntarily.

The countermeasures are behavioral, not just technical. Run regular phishing simulations so staff develop pattern recognition before a real attack arrives. Establish clear, written procedures for verifying financial requests — particularly wire transfers and invoice changes, which are common business email compromise (BEC) targets. Make reporting frictionless: a single “report phishing” button in your email client removes the friction that causes people to stay quiet when something feels off. Mandatory security awareness training, at minimum annually, should cover credential hygiene, social engineering tactics, and escalation procedures.

8. Insecure Payment Flows and PCI Non-Compliance

Payment data is the highest-value target in ecommerce. Forty percent of retail attacks in 2025 specifically targeted point-of-sale and payment systems. Some stores, in an attempt to maximize control over the checkout experience, inadvertently bring cardholder data into scope — storing it incorrectly, transmitting it over unencrypted channels, or processing it through non-compliant flows.

The foundational rule: reduce scope. Use PCI-compliant hosted payment pages or tokenization so that sensitive card data never touches your servers at all. When a customer pays via Shop Pay, Apple Pay, or Google Pay, a unique token is generated for that transaction — the actual card data never reaches your infrastructure. Shopify Payments is PSD2-compliant and offers 3D Secure Checkout, which shifts chargeback liability for fraudulent transactions from you to the card issuer. For eligible Shop Pay orders in the US, Shopify Protect covers the cost of fraudulent chargebacks entirely. Run regular vulnerability scans, follow PCI DSS controls relevant to your setup, and use certified gateways. Even small stores benefit enormously from this approach — tokenized payments and hosted checkout dramatically lower both risk and audit burden.

9. AI-Powered Bots: The Threat Most Stores Are Ignoring

This is the security challenge that didn’t exist at scale five years ago and now defines the threat landscape for ecommerce. According to the 2025 Imperva Bad Bot Report, AI-powered bad bots account for 33% of all retail web traffic. The Thales 2025 Data Threat Report found that bad bots represented 37% of all internet traffic and nearly half of all retail-specific web traffic. Between April and September 2024, retailers faced over 560,000 AI-driven automated attacks per day — including fraudulent purchase attempts, account takeover campaigns, and coordinated DDoS attacks.

These aren’t the simple bots of the past. Modern AI-powered bots mimic human browsing behavior, rotate IP addresses, pass CAPTCHA challenges, and adapt in real time. They’re used for card testing (making small purchases to validate stolen card numbers), inventory hoarding during product drops, account takeover via credential stuffing, and price scraping that undermines your competitive positioning.

On Shopify, bot protection is available as a native feature — combining industry-standard bot blocking with Shopify’s Checkpoint solution, which requires buyers to complete a human verification challenge before entering checkout. This can be activated for specific time windows (product drops, BFCM, flash sales) or left running continuously. For stores needing deeper protection, tools like Signifyd, NoFraud, and Forter layer AI-powered fraud analysis on top of platform-native defenses — analyzing hundreds of data points per transaction in milliseconds and providing financial guarantees against approved fraudulent orders.

10. No Encryption, No Backups, No Incident Response Plan

Three separate failures that often travel together — and together, they turn a manageable security incident into a catastrophic one.

On encryption: use TLS everywhere, enforce HSTS, set secure cookie flags, encrypt sensitive fields in your database, and protect backups with strong encryption using separately managed keys. Never store encryption keys in application code or config files — use a dedicated key management system. Unencrypted backups, forgotten test databases, and HTTP admin panels are low-hanging fruit that attackers find quickly.

On backups: 68% of retailers said business downtime was the most likely outcome of a cyberattack, according to VikingCloud’s 2025 survey. Ransomware specifically targets backup systems before encrypting production data. Maintain offline or immutable backups — stored separately from your primary infrastructure — and verify restore procedures on a regular schedule. A backup you’ve never tested is not a backup.

On incident response: most stores think about this only after a ransomware hit, which is too late. Build your incident response plan now. Define roles (who leads the response, who handles communications, who contacts legal and PR). Create communication templates for customer notification. Identify your legal obligations under applicable data privacy laws (GDPR, CCPA, and state-level breach notification requirements). Run tabletop exercises with your team at least once a year. The speed and quality of your response in the first 24 hours after a breach largely determines whether customers forgive you or abandon you permanently — 53% of retailers experienced lasting reputational damage following a breach.

Your Security Quick-Win Checklist

If you implement nothing else from this article today, start here. These eight actions address the most common attack paths and require no specialized expertise to execute:

• Enforce MFA for all admin accounts and staff logins — no exceptions
• Patch your platform, theme, and all apps — check for updates this week
• Tokenize payments and use hosted checkout — get card data off your servers
• Audit and limit third-party app access — remove anything you no longer use
• Set up centralized logging with alerts for failed logins and admin changes
• Run a phishing simulation with your team — awareness is your cheapest defense
• Review and remove stale staff accounts — especially former contractors and agencies
• Test your backup restore process — confirm you can actually recover from it

Security Is a Customer Trust Investment, Not a Cost Center

The financial numbers are sobering: $3.54 million average breach cost, 34% year-over-year increase in retail attacks, 53% of breached retailers experiencing lasting reputational damage. But the more important number is this: a large share of customers who experience a breach at a retailer they trusted will stop buying from that brand entirely. In DTC ecommerce, where customer lifetime value is everything, that loss compounds with every repeat purchase that never happens.

Security done right isn’t a tax on your business. It’s a competitive advantage. Stores that can credibly demonstrate they protect customer data — through transparent policies, visible security signals at checkout, and a track record of responsible data handling — build the kind of trust that converts browsers into buyers and buyers into loyal advocates.

Start with the three highest-leverage actions: enable MFA everywhere, patch your platform and apps, and stop storing card data you don’t need. Those three moves alone put you ahead of a significant share of the retail market. Then build from there — access control, monitoring, vendor governance, incident response. Each layer you add reduces your exposure and strengthens the foundation that your revenue depends on.

Frequently Asked Questions

What is the most common security mistake ecommerce stores make?

The most common security mistake is using weak or single-factor authentication for admin accounts and staff logins. Compromised credentials were linked to 55% of retail breaches in 2025. Requiring multi-factor authentication (MFA) for every account with store access is the single highest-impact security action any ecommerce operator can take. On Shopify, organization-level two-factor authentication can be enforced across all staff accounts in minutes.

How do AI-powered bots threaten ecommerce stores in 2025?

AI-powered bad bots now account for 33% of all retail web traffic, according to the 2025 Imperva Bad Bot Report. These bots mimic human behavior to conduct card testing (validating stolen credit card numbers through small purchases), account takeover via credential stuffing, inventory hoarding during product drops, and DDoS attacks timed to peak sales windows. Unlike earlier bots, AI-driven bots can rotate IP addresses, pass CAPTCHA challenges, and adapt to detection systems in real time. Shopify’s native bot protection and Checkpoint solution, combined with third-party tools like Signifyd or NoFraud, provide the layered defense needed to counter these threats.

How can a Shopify store protect itself from payment fraud?

The most effective approach is to reduce your payment data footprint entirely. Use Shopify Payments with 3D Secure Checkout, which shifts chargeback liability to the card issuer for fraudulent transactions. Enable Shop Pay, Apple Pay, or Google Pay — these payment methods use tokenization, meaning actual card data never reaches your servers. Shopify Protect automatically covers eligible Shop Pay orders in the US against fraudulent chargebacks. For additional protection, deploy an AI-powered fraud detection tool like NoFraud or Signifyd that analyzes hundreds of transaction signals in real time and provides a financial guarantee on approved orders.

What should an ecommerce incident response plan include?

An effective ecommerce incident response plan should define clear roles (who leads the response, who handles customer communications, who contacts legal counsel and PR), include pre-written communication templates for customer and regulatory notification, identify your legal obligations under applicable data privacy laws (GDPR, CCPA, and state breach notification statutes), and outline step-by-step recovery procedures. The plan should be tested through tabletop exercises at least annually. Critically, it should include procedures for isolating affected systems, preserving evidence for forensic investigation, and restoring from verified offline or immutable backups. The faster and more organized your response in the first 24 hours, the better your chances of retaining customer trust.

How often should ecommerce stores review their security settings?

At minimum, conduct a formal security review quarterly. This should include an access audit (removing stale accounts and reviewing permissions), a check for outstanding platform and plugin updates, a review of active third-party integrations and the data they can access, and a test of backup restore procedures. More frequent checks — monthly or after any significant platform change, new app installation, or personnel transition — are strongly recommended. For stores processing high transaction volumes, continuous monitoring via centralized logging and automated alerting should replace periodic manual reviews as the primary detection mechanism.