How to Get Shopify VAT Numbers Into Your Accounting Software

TL;DR: Shopify doesn’t natively pass validated VAT numbers to accounting software. To get VAT IDs onto invoices in tools like Billbee, sevDesk, Exact Online, or Xero, you need them stored as order attributes. The EU Tax Exemption app validates VAT numbers via VIES and saves them to every order automatically, so your accounting stack can pick them up without manual work.

The Problem: VAT Numbers Get Stuck in Shopify

You validate a customer’s VAT number. The order gets tax-exempt status. But when your accounting software pulls the order, the VAT number is nowhere to be found.

This is one of the most common frustrations for B2B Shopify sellers in Europe. Shopify can mark a customer as tax-exempt, but that status alone doesn’t tell your invoicing tool which VAT number justified the exemption. And without the VAT number on the invoice, your reverse charge invoice isn’t compliant.

The fix is straightforward: the VAT number needs to be stored as an order attribute (note_attributes) that your accounting software can read. That’s exactly what the EU Tax Exemption app does automatically for every validated B2B order.

Below is a practical guide for connecting that data to the most popular European accounting and invoicing tools.

How It Works: The Data Flow

Before diving into specific tools, here’s what happens behind the scenes:

1. Customer enters their VAT number at checkout (or via the storefront widget)
2. The number is validated against the EU VIES database in real time
3. Tax exemption is applied to the order (reverse charge or full exemption)
4. The validated VAT number is saved as a vat-id order attribute in Shopify
5. Your accounting software reads that attribute when it syncs the order

The key is step 4. Without the VAT number stored on the order itself, your accounting tool has nothing to grab. Let’s look at how each tool handles this.

Billbee

Billbee is the go-to multichannel order management tool for German and Austrian Shopify sellers. It handles invoicing, shipping labels, and accounting exports, including DATEV.

Billbee reads Shopify’s order note_attributes by default. Once the EU Tax Exemption app saves the VAT number as a vat-id attribute, Billbee picks it up automatically during order sync.

Setup:

• In Billbee, go to Settings and then Invoice Templates
• Add the VAT ID field placeholder to your invoice template
• Billbee maps the vat-id from Shopify’s additional details to the customer’s tax number field
• Reverse charge invoices are generated automatically when the VAT ID is present and the customer is from a different EU country

Billbee also exports to DATEV format, so the VAT number flows all the way through to your tax advisor.

sevDesk

sevDesk is popular with small and mid-sized German businesses for bookkeeping, invoicing, and tax filing. Their Shopify integration syncs orders directly into sevDesk and creates invoices automatically.

Setup:

• Connect sevDesk to Shopify via their app or through Billbee as a middleware
• sevDesk reads the customer’s VAT ID from the order’s additional details
• In your sevDesk invoice settings, enable the reverse charge notice for EU B2B invoices
• The VAT number appears on the generated invoice alongside the 0% VAT line

If you use sevDesk through Billbee, the VAT number passes through both systems. If you use sevDesk’s direct Shopify integration, make sure it’s configured to read note_attributes.

lexoffice (Lexware Office)

lexoffice is another major German cloud accounting tool, especially popular with freelancers and small businesses. Their Shopify app syncs orders and creates bookkeeping entries.

Setup:

• Install the lexoffice Shopify app from the App Store
• The app imports orders with their note_attributes, including the vat-id
• In lexoffice, the VAT ID is linked to the customer contact record
• When generating invoices, lexoffice includes the customer’s VAT number and applies the correct reverse charge treatment

lexoffice also handles the EÜR (Einnahmenüberschussrechnung) and VAT returns, so having the VAT number on the order makes your tax filings more accurate from the start.

DATEV

DATEV isn’t something you use directly. It’s the standard format German tax advisors use. Your accounting tool needs to export Shopify data in DATEV-compatible format, and the VAT number needs to be part of that export.

How to get VAT numbers into DATEV:

• Via Billbee: Export orders in DATEV format. Billbee includes the VAT ID from order attributes in the export file
• Via sevDesk: sevDesk generates DATEV-ready exports with customer VAT numbers attached
• Via lexoffice: lexoffice exports are DATEV-compatible and include VAT IDs
• Via Pathway Accounting Export Pro: Dedicated Shopify-to-DATEV app that reads note_attributes

The common thread: all of these tools need the VAT number to be stored on the Shopify order. Without it, your DATEV export has a gap that your Steuerberater will flag.

Exact Online

Exact Online is the dominant accounting platform in the Netherlands and Belgium. Many Dutch Shopify sellers use it for their complete financial administration, including BTW-aangifte (VAT returns).

Setup:

• Use a connector like Sherpaan, Marello, or a custom Zapier/Make integration to sync Shopify orders to Exact Online
• Map the vat-id order attribute to the “BTW-nummer” field on the Exact Online contact
• When Exact generates invoices, it pulls the VAT number from the contact record and applies the correct ICL (intracommunautaire levering) tax code

For Dutch sellers: the VAT number is required on your ICP-opgave (EC Sales List). Having it flow automatically from checkout to Exact saves you from manually cross-referencing orders at the end of each quarter.

Moneybird

Moneybird is a popular Dutch and Belgian cloud accounting tool known for its clean interface and strong VAT handling. Many smaller Dutch Shopify stores use it.

Setup:

• Connect Shopify to Moneybird via their API or a connector like Zapier
• Map the vat-id order attribute to Moneybird’s “BTW-nummer” contact field
• Moneybird automatically applies the “Levering/dienst naar landen binnen de EU (intracommunautair)” tax rate (0%) when a valid EU VAT number is present
• The VAT number appears on the generated invoice with the correct reverse charge notice

Moneybird also generates the ICP declaration data you need for your quarterly VAT filing with the Belastingdienst.

e-Boekhouden

e-Boekhouden is a widely used Dutch accounting platform, particularly among ZZP’ers and small businesses. It’s affordable and handles Dutch VAT requirements well.

Setup:

• Use a connector or webhook-based integration to push Shopify order data to e-Boekhouden
• Include the vat-id from the order’s note_attributes in the customer record
• e-Boekhouden uses the VAT number to determine the correct tax treatment for intracommunautaire leveringen

Xero

Xero is widely used across the UK, Ireland, and increasingly in other European markets. It handles multi-currency and VAT well, making it a solid choice for cross-border B2B sellers.

Setup:

• Use a Shopify-Xero connector (A2X, Amaka, or Zapier)
• Map the vat-id order attribute to Xero’s “Tax Number” field on the contact
• Set up a “Zero Rated EC Goods” or “Reverse Charge” tax rate in Xero for qualifying B2B orders
• The VAT number appears on invoices and in your EC Sales List report

For UK sellers post-Brexit: the same workflow applies, but you’ll map to HMRC-validated tax numbers instead of VIES.

QuickBooks

QuickBooks Online is used by Shopify sellers across Europe, especially in the UK and France. Its VAT handling has improved significantly in recent years.

Setup:

• Connect Shopify to QuickBooks via a connector like A2X, Webgility, or MyWorks
• Map the vat-id order attribute to the customer’s “VAT Registration Number” field
• Set the appropriate VAT code (RC for reverse charge) on qualifying invoices
• QuickBooks includes the VAT number on invoices and in your Making Tax Digital (MTD) submissions for UK sellers

Sufio

Sufio is built specifically for Shopify invoicing and handles EU VAT compliance natively. It’s particularly popular with merchants who need professional, multilingual invoices.

Setup:

• Sufio reads the vat-id from Shopify order attributes automatically
• It generates compliant reverse charge invoices with the customer’s VAT number, 0% VAT line, and the required “VAT reverse charge” notice
• Invoices can be sent automatically when orders are placed or fulfilled
• Supports PEPPOL e-invoicing for the upcoming 2027 EU e-invoicing mandates

If you don’t use a separate accounting tool and just need compliant invoices from Shopify, Sufio combined with our app covers the full workflow.

Quaderno

Quaderno specializes in tax compliance for digital and physical goods across the EU. It automatically detects B2B transactions and applies the correct tax treatment.

Setup:

• Quaderno connects to Shopify and reads customer tax IDs from order data
• It determines whether an order qualifies for reverse charge based on the validated VAT number and the countries involved
• Generates tax-compliant invoices and credit notes automatically
• Provides ready-to-file tax reports for multiple EU jurisdictions

FastBill

FastBill is a German invoicing and accounting tool often used by freelancers and small businesses. It handles GoBD-compliant invoicing and DATEV exports.

Setup:

• Connect Shopify to FastBill via Zapier or a direct API integration
• Map the vat-id to FastBill’s “USt-IdNr.” customer field
• FastBill generates reverse charge invoices with the customer’s VAT number and exports to DATEV

What All These Integrations Have in Common

Every tool in this list needs the same thing: the VAT number stored on the Shopify order in a machine-readable format. The specific field mapping varies, but the principle is identical.

Shopify’s native VAT validation (available on Shopify Tax) can check whether a number is valid, but it doesn’t write the VAT number to order attributes. That means your accounting software can’t access it through the normal order sync. As of early 2026, the VAT ID from Shopify’s native validation still isn’t exposed via the Admin API.

The EU Tax Exemption app bridges this gap. It validates via VIES, applies the tax exemption, and stores the VAT number as a vat-id note_attribute on the order. That attribute is readable by every accounting tool that syncs with Shopify, including all the ones listed above.

Quick Reference: Tool and Field Mapping

Accounting Tool	Country	Shopify Field	Target Field
Billbee	DE/AT	note_attributes (vat-id)	Tax number / USt-IdNr.
sevDesk	DE/AT	note_attributes (vat-id)	USt-IdNr. on contact
lexoffice	DE/AT	note_attributes (vat-id)	USt-IdNr. on contact
DATEV (via export)	DE/AT	note_attributes (vat-id)	Debitor tax number
Exact Online	NL/BE	note_attributes (vat-id)	BTW-nummer on contact
Moneybird	NL/BE	note_attributes (vat-id)	BTW-nummer on contact
e-Boekhouden	NL	note_attributes (vat-id)	BTW-nummer on contact
Xero	UK/EU	note_attributes (vat-id)	Tax Number on contact
QuickBooks	UK/EU	note_attributes (vat-id)	VAT Reg. Number
Sufio	EU-wide	note_attributes (vat-id)	Auto-detected
Quaderno	EU-wide	note_attributes (vat-id)	Tax ID on contact
FastBill	DE	note_attributes (vat-id)	USt-IdNr.

Getting Started

The setup takes about two minutes. Install the EU Tax Exemption app, and every validated B2B order will have the VAT number stored on it. From there, your accounting software does the rest.

If you’re not sure which VAT validation app fits your setup, or you want to understand how reverse charge works in Shopify, we’ve covered both in detail.

The bottom line: your checkout handles the tax exemption, but your books need the VAT number. Make sure the data actually gets there.