The Most Common E-Commerce Website Vulnerabilities and How to Deal with Them

Date
December 16, 2025
Reading Time
4 minute read

The rapid growth of e-commerce in the Philippines has opened up exciting opportunities for entrepreneurs. With more shoppers turning to online platforms for convenience, businesses can reach a wider audience than ever before. But this digital boom comes with an equally fast-growing risk: cybercriminals targeting vulnerable online stores.

Security breaches in e-commerce don’t just lead to substantial financial loss. They can compromise sensitive customer data, erode hard-earned trust, and tarnish your brand’s reputation—damage that’s far harder to repair than a broken website. Customers today expect secure, seamless transactions as a basic standard, not a premium feature, and your competitors stand ready to provide them with that experience if you can’t.

The good news? It’s possible to armor your online store against the most common vulnerabilities with the right precautions and tools. We at Maya are here to walk you through current best practices regarding online safety and security in the e-commerce space, as well as provide you with top-tier business management solutions to optimize your operations accordingly. Let’s talk about common security liabilities for e-commerce stores and what you can do about them.

Unsecured Payment Processing

When your customers enter payment details on your site, they’re trusting you with some of their most sensitive information. If you don’t do your due diligence to protect those transactions, you risk exposing that data to theft or fraud. Beyond the immediate financial implications, a single incident can have long-term consequences for your reputation and customer loyalty.

Using a PCI DSS-compliant payment gateway significantly reduces this risk. Maya Checkout offers end-to-end encryption, real-time fraud protection, and support for a wide range of payment methods, from credit and debit cards to popular e-wallets and QR Ph. When you integrate the best payment gateway available into your store, you’re not only streamlining checkout for your customers but also improving your security posture in ways that help protect both sides of the transaction.

Weak or Reused Passwords

One compromised password can be all it takes for an attacker to gain control over your admin panel, change site settings, or steal customer information. Weak credentials—short, predictable, or reused across accounts—are particularly easy to crack with automated tools. Multiple accounts may have elevated permissions on an e-commerce site, so this vulnerability can escalate quickly.

To mitigate the risk, establish a strong password policy for your team and enforce it for all staff accounts. Use two-factor authentication for administrative logins, and encourage customers to create secure passwords with a strength meter at sign-up. For your internal team, consider using a reputable password manager to maintain complex, unique logins without the hassle of memorizing them all.

Outdated Software and Plugins

Cybercriminals often look for weaknesses that are already well-documented, and outdated e-commerce platforms, themes, or plugins can be a goldmine. Once a vulnerability becomes public, attackers actively scan the internet for sites that haven’t installed the necessary patches. Even a single neglected update can create an entry point for malware or data theft.

Stay ahead by scheduling regular update checks for your entire tech stack, from your content management system to every installed extension. Where possible, enable automatic security updates, and remove any plugins or tools you no longer use. This reduces the number of potential vulnerabilities while keeping your site aligned with the latest performance and security standards.

Attacks via Cross-Site Scripting (XSS) or SQL Injection

A well-placed malicious command or script can do serious damage to an e-commerce site. In SQL injection attacks, for example, hackers exploit insecure form fields or URLs to access or manipulate your database. With XSS, they inject harmful scripts into your web pages that can hijack user sessions, steal data, or send visitors to illicit external websites.

Defense starts with secure coding practices. Ensure your development team uses parameterized queries for database interactions and validates all user input before processing it. Implement a Content Security Policy (CSP) to control what scripts can run on your site, and regularly audit your site for vulnerabilities using trusted scanning tools.

Poor Access Controls and Lack of Monitoring

Sometimes, the greatest risk isn’t from outside attackers but from within your own operations. If you grant staff or third-party service providers more access than they need, you may just open the door to accidental misconfigurations or deliberate abuse. Without proper monitoring, you might not even notice unusual activity until significant damage has been done.

In business, the practice of giving each account only the permissions necessary for its role is known as the principle of least privilege. Review access rights on a set schedule, especially after staff changes or project completions. Complement these controls with active monitoring—log key activities, set up real-time alerts for suspicious actions, and maintain secure, offsite backups so you can recover quickly if something does go wrong.

Top-of-the-Line Business Solutions for Seamless E-Commerce

With the right tools, it’ll be easier than you think to level up operations at your online store. Maya Checkout, the best payment gateway for small businesses in the Philippines, is just the tip of the iceberg. Sign up for Maya Business to gain access to our full suite of payment and business banking solutions, which have been expressly designed to help teams at startups and SMEs do their best work.

Opening your own Maya Business account lets you set up a Maya Business Deposit account and use it as your settlement account. With an industry-leading 2.5% per annum interest rate, you’ll earn PHP 25,000 in interest per year on a PHP 1 million deposit. You can also send money to your partners and suppliers for free via InstaPay and PESONet, which means you’ll be saving more in the long run. 

Signing up also qualifies you for a no-collateral Maya Flexi Loan offer of up to PHP 2 million in just 3 months—that’s more funding you can use to develop your business even more. Just use Maya as your primary processor for all wallet and card payments. The more you use our solutions, the better the loan offer will be. 

Sign up for your own Maya Business account today and enjoy all these benefits right out of the box!