This guide walks you through connecting the Fakturoid app to your Shopify store and completing the setup that matters most. The whole process takes about 5 minutes — the video above covers everything below if you'd rather watch.
Before you begin
You'll need:
An active Fakturoid.cz account on one of their plans. The app is a connector between Shopify and Fakturoid — it doesn't replace either.
Admin access to your Shopify store.
To know whether you're a non-payer, identified person, or VAT payer. If you're not sure, check with your accountant first — this affects several setup steps.
Step 1: Connect to Fakturoid
On the app's Home page, click Connect to Fakturoid.
Log in to your Fakturoid account.
Click the yellow button to grant access to the app.
After a few seconds, you'll be redirected back to the app.
Once connected, the app will display the name of your Fakturoid account so you can confirm the connection.
💡 Multiple Fakturoid accounts under the same email? The app always connects to whichever account is marked as default in Fakturoid. To switch, change the default in your Fakturoid user settings, then disconnect and reconnect the app.
Step 2: Check your Fakturoid setup
Before configuring the app, make sure these are set up in Fakturoid:
Billing details — Your business information and your VAT status (non-payer, identified person, or VAT payer).
Bank and payment matching — Link your bank account. This is especially important if you plan to use proforma invoices, since payment matching is what triggers the final invoice.
Step 3: Configure VAT in Shopify
The app does not calculate tax — it forwards whatever Shopify sends to Fakturoid. So your VAT setup needs to be correct in Shopify, and consistent with your Fakturoid setup. In Shopify, go to Settings → Taxes and Duties and review both your global tax settings and your tax regions, including OSS if you sell across the EU.
A misconfigured VAT setup is the single most common reason invoices fail to create. See the VAT settings guide for your specific scenario (non-payer, micro-business under €10k, OSS, country-by-country, or B2B reverse charge).
Step 4: Configure the app
General
Invoice creation delay — A buffer between order creation and invoice creation. We recommend 1–2 minutes, especially if you use Cash on Delivery, Shopify Flow, or other apps that modify orders right after checkout.
Tags — Optionally add tags to Shopify orders and to Fakturoid invoices once an invoice is created. Useful for at-a-glance status.
Notification emails — Email address(es) where the app will send error notifications if an invoice fails to create.
Invoicing rules
Bank account — Choose which Fakturoid bank account appears on the invoice.
Invoice creation timing — Configurable per payment method: on order creation, after payment, proforma + final, or on fulfillment. See Fakturoid invoice creation rules.
Order change behavior — When an order is edited (refund, item change), the app can either issue a correction tax document (recommended for VAT payers) or update the existing invoice (for non-payers). See Order change behavior.
Send invoice emails from Fakturoid — When enabled, Fakturoid emails the customer the invoice (optionally as a PDF) once it's created. See How to send an invoice email automatically.
OSS special arrangement — If you use the OSS regime, enable it here as well as in Shopify. Both sides need to match.
POS customer — If you accept POS orders, Fakturoid still requires every invoice to have a customer. Create a dummy customer (e.g. "Retail Sale") in Fakturoid and paste its ID here. See Identify the customer for POS orders.
Invoice details
Fields shown on the invoice — Optional toggles for SKUs, payment ID, authorization code, and similar.
Variable symbol — Use the invoice number, order number, or a custom value pulled from order attributes. See Custom variable symbol.
Numbering series — By default the app uses whatever series is set as default in Fakturoid. If you run multiple stores with separate numbering, paste the series ID here. See Invoice numbering.
Step 5 (optional): Add the invoice link to your Shopify confirmation email
You can embed a direct invoice link into Shopify's own order confirmation email, so customers can access the invoice from the email they already receive. See How to add the invoice link to the Shopify order confirmation email.
You're all set!
Once an invoice is created, you can click through to it directly from the Shopify order. To create an invoice manually — for example for a missed order or a historical one — open the order and choose More actions → Create invoice. To do several at once, select multiple orders in the orders list and use the same action. (Manual creation works for orders up to 60 days old, with a maximum of 50 at a time.)
A few useful things to know as you go:
If invoice creation fails, you'll get an email at the address set in General Settings. See Invoice creation errors: causes and solutions.
To skip invoice creation for a specific order, tag it
fakturoid-no-invoicein Shopify before the invoice generates.
Have any questions? We're here to help! Use the in-app chat, our support team is happy to assist.