Avoiding Accounting Mistakes: The 5 Most Common Errors in E-Commerce – And How to Prevent Them

Running an online store – whether on Amazon FBA, Shopify, WooCommerce, or other platforms – comes with logistical and operational challenges. But it also demands rigorous accounting. The sheer volume of transactions, the variety of platforms, and the complexity of tax regulations make e-commerce accounting a minefield. The good news: most mistakes can be avoided with smarter workflows and automation.

One of the most common – and costly – mistakes is improper or non-compliant document archiving. Many merchants simply save invoices as PDFs or rely on their shop system’s archive feature, without checking if these meet legal requirements. According to § 146 of the German Fiscal Code (AO), entries must be recorded individually, completely, accurately, in a timely manner, and in an orderly fashion. These criteria are central to the GoBD – the German principles for proper accounting and digital recordkeeping.

A GoBD-compliant accounting system must above all ensure traceability and verifiability. That means: every financial transaction must be backed by a proper invoice – without exception. It must also guarantee timely booking and recording. Cash transactions must be documented daily, and non-cash receipts must be booked within ten days. Accuracy is equally essential: transactions must reflect real economic activity, use proper account classification, and be recorded in a structured way. Immutability is another critical pillar: once data has been recorded, it must not be altered. Any corrections must be clearly documented and traceable to the original entry. Completeness is also required: every document must include unique identifiers, date, amount, quantity, and the names of both parties involved. Finally, the principle of order dictates that all bookkeeping must be systematic, logical, and understandable by third parties. Invoice numbers must never be reused, and cash income must be clearly separated from card or digital payments.

A tool like KudTax ensures full GoBD compliance by automatically archiving all documents in a structured, immutable format, while ensuring completeness and full traceability from invoice creation to export.

Another common pitfall is incorrect tax key assignment. In cross-border shipping, OSS use, or intra-EU deliveries (e.g. via Amazon FBA), tax obligations quickly become complex. Merchants who rely on outdated tools or manual entries often end up reporting incorrect VAT. These mistakes typically surface during audits – and can result in back taxes or penalties.

KudTax uses transaction-level logic to automatically identify the correct VAT regime and applies the proper tax codes – including reverse charge and third-country scenarios.

Misalignment between payments, documents, and orders is another source of error. If you collect payments through Stripe or PayPal but manage your invoices separately in Shopify or Amazon, things can spiral out of control. When records can’t be matched, documents remain unaccounted for and transactions are improperly recorded – compromising your tax accuracy.

With intelligent reconciliation, KudTax matches payments to the correct invoice and order automatically and traceably.

Another underestimated risk is Amazon FBA warehousing logistics. Many sellers don’t realize that Amazon frequently transfers goods between EU countries – for example, to Poland, the Czech Republic, or France. These "intra-community movements" trigger VAT obligations and often require VAT registration in each destination country. If such transfers aren’t detected and reported properly, merchants can violate reporting obligations and face steep tax consequences.

KudTax automatically detects FBA stock movements and reflects them correctly in your accounting exports and tax records.

Finally, many merchants underestimate the risks and workload involved in manual exports. Pulling data individually from Amazon, Shopify, PayPal, and other platforms – then managing them in spreadsheets – creates a huge administrative burden and high error potential. Typos, missing documents, and inconsistent formats are common.

KudTax eliminates that burden by offering standardized, fully automated exports for DATEV, Xero, Lexware, Stotax etc. and tax advisors – with accurate booking entries and proper account mapping.

In short: E-commerce bookkeeping is full of hidden risks – but it doesn’t have to be stressful. With the right automation, you avoid costly mistakes, stay compliant, and save both time and money.

Start with KudTax today – and turn your e-commerce bookkeeping from a liability into a competitive advantage.