What to report in your VAT Return: most common oversights

What to report in your VAT Return: most common oversights 

Accurate VAT reporting is one of the most challenging aspects of cross-border compliance. Many errors do not arise from incorrect rates or miscalculations but from transactions that are missing entirely from the VAT return. 

With the growing complexity of cross-border trade, marketplaces and fulfilment networks, companies often struggle to identify what needs to be reported and where. Tax authorities across Europe are increasing data matching between customs systems, marketplace reports and VAT returns, making it more important than ever to ensure every transaction type is correctly captured. 

Some of the most common oversights are shown below, illustrated with examples and best practices to help ensure compliant reporting. 

1. Sales transactions: reporting everything you need to
2. Marketplace Sales

When selling via online marketplaces such as Amazon, eBay or Zalando, many Non-EU sellers assume that if the marketplace collects and remits VAT, there is nothing further to report. 

However, this is not correct. Even when the marketplace is deemed the VAT supplier, the seller must still report the zero-rated deemed sale to the marketplace in their own VAT return. 

Failure to do so leads to incomplete VAT records and mismatches between declared turnover and platform data. 

1. Direct sales (from your website or B2B)

For direct website or B2B sales, businesses remain responsible for charging and reporting VAT under the correct place of supply rules. This includes both domestic and cross-border transactions. 

Misapplication of VAT rates or failure to recognise the correct reporting country are common issues, especially for businesses with mixed B2B and B2C operations. 

2. Purchase transactions: reporting reverse charges
3. Intra-EU acquisitions and domestic reverse charge

One of the most frequent errors occurs when companies exclude purchases with no VAT on the invoice. 

For example, an intra-EU acquisition from a supplier in Germany to a company in France will have no VAT charged by the supplier.  However, the French company must self-account for VAT under the reverse charge mechanism. 

These transactions must appear in both the output and input boxes of the VAT return, provided that the purchases are used for the companies’ taxable activities. 

Failure to do so underreports turnover and VAT, exposing the company to penalties and compliance queries. 

1. Services from non-EU suppliers

Services purchased from non-EU providers, such as software, digital services or consultancy, are also subject to reverse charge. Many companies overlook this, particularly where invoices do not show VAT. 

The correct procedure is to declare VAT as due and reclaim it in the same return (if fully recoverable). 

3. Import VAT: reclaiming what you pay

Import VAT is another area where reporting inconsistencies frequently occur. 

In many cases, logistics providers or customs agents pay import VAT on behalf of the importer. Businesses often do not receive the supporting documentation, meaning they fail to record or reclaim it. 

Best practice is to obtain all customs import declarations  to verify the VAT amount paid and ensure it appears in the return. 

In some countries, such as the Netherlands and Belgium, import VAT may be handled via postponed accounting or reverse charge, rather than payment at the border. In these cases, the VAT must still be declared, even if no physical payment is made. 

Example: limited fiscal representation in the Netherlands 

When a non-EU business uses a limited fiscal representative to import goods into the Netherlands and then ship onwards to another EU country, the representative reports the import using its own Dutch VAT number. 

However, the client must still report the intra-EU arrival in the destination country. Many companies fail to do so because they lack the invoices from the representative or do not realise the reports are required. 

4. Reporting transfers and warehousing movements

E-commerce sellers and fulfilment-based businesses increasingly use multiple warehouses across Europe to shorten delivery times. 

However, transferring own goods between countries creates VAT obligations similar to regular cross-border sales.  Each movement should be recorded as: 

• A deemed supply in the country of dispatch, and 

• A deemed acquisition in the country of arrival. 

Relying solely on data from platforms such as Amazon can be risky, as these reports often exclude cost prices required for Intrastat and VAT reporting. 

A complete VAT data system should integrate inventory management, transport documentation, and accounting data to ensure every movement is correctly reflected in the VAT return. 

5. Supporting reports: VAT, Intrastat and compliance

Beyond VAT returns, businesses must also submit additional reports such as: 

• Intrastat declarations: which require transport and delivery details not found on invoices; 

• EC Sales Lists: detailing B2B intra-EU transactions 

• Discrepancies between these reports can trigger audits or compliance reviews. Ensuring data consistency across all reporting systems is a hallmark of robust VAT compliance. 

6. Best practices for VAT reporting

To avoid missing or underreported transactions, companies should adopt the following practices: 

1. Map all transaction types: Identify where each transaction is recorded (ERP, marketplace, logistics provider). 

1. Include zero-VAT and reverse-charge items: Absence of VAT on the invoice does not mean it should be excluded. 

1. Collect and store import documentation: Coordinate with logistics partners and fiscal representatives to obtain all records. 

1. Cross-check systems: Reconcile VAT returns with customs data, Intrastat  and sales reports. 

1. Review marketplace data critically: Supplement Amazon or other marketplace data with internal cost and transport data. 

1. Centralise reporting: Use an integrated compliance platform that captures all relevant data types and transaction flows. 

1. Educate accounting teams: Ensure all staff involved in VAT preparation understand which transactions require reporting, even if no VAT is shown. 

7. Visibility is key to compliance

Incomplete VAT returns often stem from gaps in understanding rather than deliberate errors. The complexity of modern supply chains that covers marketplaces, fulfilment centres and third-party logistics providers, creates situations where key data sits across multiple systems or entities. 

By ensuring that all relevant transactions are identified, verified, and reported, businesses can maintain compliance, recover VAT efficiently, and reduce the risk of costly audits. 

At Tax Desk, we support clients by identifying missing data, reconciling multiple sources, and ensuring all transactions are correctly included in VAT returns across 60+ jurisdictions. Our technology flags gaps early, and our team provides professional guidance to resolve them. 

In VAT reporting, accuracy is not just about numbers — it’s about visibility. And the more visibility you have, the stronger your compliance will be. 

Download our guide to learn more : What to report in your VAT Return – most common oversights