What is an eCommerce audit? A 2025 guide for EU-linked stores

If you run an eCommerce business (or work in one), you’ve probably had that gut-dropping moment at 2 a.m. when you realize that something has gone seriously wrong. Perhaps a major promotional campaign has failed, customers are complaining about failed payments, or worse, you open your inbox to find a very polite (but terrifying) email about PCI DSS, GDPR, or missing documents from a tax authority.

If that hasn’t happened to you yet… give it time. It will.

Most of us only start digging when the fire alarm is already screaming. An eCommerce audit is the boring-sounding thing nobody wants to do — until they desperately wish they had. It’s basically the yearly physical for your store: catch the little problems while they’re still cheap and painless, instead of doing open-heart surgery later when investors, lawyers, or the press are watching.

TL;DR (Key Insights):

• An eCommerce audit is a structured online store audit of security, payments, compliance, fraud, and continuity.

• It focuses on eCommerce platform security, online payment security audit & PCI DSS compliance, and customer data protection eCommerce (GDPR, ISO 27001/27701).

• It also covers zero trust architecture eCommerce, eCommerce business continuity, and eCommerce fraud prevention & security awareness.

• In practice, it’s what kept platforms like PRSNT, LENSA, and Kupatana stable during high-traffic campaigns, mobile-driven revenue, and millions of monthly users.

What is an eCommerce audit?

An eCommerce audit is a structured review of your platforma eCommerce — website, mobile app, ERP, payment gateways, marketing tools, and logistics systems — treated as one connected system. It’s the digital equivalent of auditing in commerce: not just looking at numbers, but analysing how the whole machine behaves under load, during campaigns, and under regulatory pressure.

A good eCommerce audit gives you a clear, executive-level view of:

• where you are exposed (security, PCI DSS, GDPR, vendor/API risk),

• where you leak revenue (failed payments, checkout friction, unstable UX), and

• what must be fixed first (a prioritized roadmap, not a random ticket list).

Whether you run a custom stack or perform a Shopify audit, the goal is the same: understand your real risk surface and fix the issues that matter most for revenue, trust, and compliance.

Market reality for EU-linked stores

eCommerce is doing really well in Europe at the moment, which is great for business. Solely the B2C eCommerce turnover rose 7% in 2024 to about €842 billion, which means more orders, more payment volume, and more third-party tools plugged into every store. 

But there’s a catch with this growth – it also opens up more space where things can go wrong:

• cybersecurity exposure (from e-skimming to account takeover),

• regulatory pressure (GDPR, PCI DSS, PSD2/SCA, NIS2, DORA), and

• operational risk (payment outages, logistics bottlenecks, data loss).

Zooming in on Central and Eastern Europe, Moldova and Romania show how this plays out in practice. In Moldova, online sales of products and services reached about €358.6 million in 2023, with 15.2% year-on-year growth and several hundred active online stores. In Romania, the eCommerce market reached €7.7 billion in 2024 and is expected to surpass €8 billion in 2025, growing around 8% annually (translation: both markets are growing faster than many teams can reorganise their systems).

On paper, this looks purely positive. In reality, many EU-linked merchants here are still juggling a patchwork of legacy ERPs, courier portals, custom plugins and manual reconciliations (think: “it works, but nobody fully owns the whole flow”). As cross-border orders grow, customers and partners expect EU-level reliability and compliance, no matter how young or fragmented the underlying stack is.

An audit is not a checklist. It reveals the issues that can realistically stop revenue or block growth. — Olga Petrașcu, Commercial Business Partner, EBS Integrator

In this context, every new integration, campaign, or payment method adds both upside and fragility (more moving parts = more ways something small can break at the worst time). A single misconfigured API, unpatched plugin, or missing data-processing agreement can turn into a revenue-stopping incident.

The Big 5 of an eCommerce audit

A practical eCommerce audit framework usually covers five pillars of digital commerce security and online merchant risk management:

• Platform security & eCommerce vulnerability assessment

• Online payment security audit & PCI DSS compliance eCommerce

• Customer data protection eCommerce (GDPR, ISO 27001/27701)

• Zero trust architecture & eCommerce business continuity

• eCommerce fraud prevention & security awareness training

Skip one, and it tends to explode later — usually during peak season or a regulator review.

eCommerce vulnerability assessment

This part of the audit looks at online retail cybersecurity: how your shopping experience behaves under real-world pressure. A solid eCommerce vulnerability assessment will:

• map critical flows from catalog to checkout and order confirmation;

• inspect checkout page vulnerabilities and third-party scripts (e-skimming, Magecart-style attacks);

• review shopping cart security and merchant account security in admin;

• test key APIs and plugins against common OWASP issues.

On the PRSNT gift-giving application, we refactored an unfinished MVP, addressed GDPR gaps, and rebuilt integrations to prevent campaigns from breaking the system. The result: an automated promo sent 12,000+ gifts without checkout failures or data exposure — a clear example of eCommerce security ROI and online sales protection.

Online payment security audit & PCI DSS compliance

For most retailers, payments are where security, regulation, and revenue collide. An online payment security audit typically checks:

• how card and wallet data flow from browser/app to PSP and back;

• PCI DSS v4.0 requirements on script inventory and tamper monitoring for payment pages;

• tokenization and encryption boundaries;

• payment gateway compliance across PSPs, acquirers, and local methods.

It also reviews PSD2 Strong Customer Authentication (SCA) and 3DS2 setups: routing, exemptions, and failure handling. Done well, this becomes eCommerce conversion optimization security — staying compliant without messing up approvals or UX.

What is ISO 27001, 27701 for eCommerce? (EU Standards)

For online retail, the most relevant ISO standards for e-commerce are:

• ISO 27001 — information security management;

• ISO 27701 — privacy and PII management on top of 27001.

An audit aligned with ISO 27001 certification in Romania eCommerce checks access control, backup/restore, logging, incident response, and vendor DPAs against these expectations.

But that's not all of it.

On top of ISO, a serious eCommerce regulatory compliance review tracks:

• GDPR: consent, cookie governance, data-subject rights, 72-hour breach process;

• NIS2: EU-wide baseline for cybersecurity risk management and reporting, as summarized by ENISA’s guidance on NIS2 implementation;

• DORA: operational resilience for finance-linked services and ICT providers, described in EIOPA’s overview of the Digital Operational Resilience Act.

For retailers embedding payments, BNPL, or financial products, these rules increasingly shape how “good enough” security looks.

Zero trust, continuity & fraud

A zero trust architecture eCommerce approach assumes no automatic trust: payment, PII, and admin zones are segmented; MFA and least-privilege access are enforced; and access is logged and monitored.

From there, eCommerce business continuity asks:

If a PSP, cloud region, or key integration fails during a campaign, how fast does checkout recover — and have we tested it before Black Friday?

For the LENSA digital optical showroom, we helped build a mobile-first channel that now drives roughly 40% of total sales. At that point, continuity and segmentation aren’t “IT extras” — they are core to online sales protection and customer trust in eCommerce.

On the human side, eCommerce fraud prevention and cybersecurity awareness cover:

• credential stuffing and account takeover;

• promo and coupon abuse;

• card-not-present fraud and chargebacks;

• business email compromise risks in finance and ops.

The ROI of an eCommerce audit

For executives, the question behind all this is simple:

Does it pay off?

A well-run eCommerce audit reduces eCommerce data breach costs, improves stability, protects customer trust, and delivers a ranked roadmap of fixes — from platform hardening and PCI work to ISO-aligned processes and awareness training.

If you’re not sure where to start, the most efficient entry point is a structured business analysis + eCommerce audit: mapping your processes, platforms, and regulatory exposure in one view. That’s exactly what our Business analysis for eCommerce and retail service is designed to do — align technology, risk, and growth priorities before you commit budget to the wrong problems.