Shopify and Moloni ON: Automate your invoicing

Running a successful online store requires focus on sales, marketing, and customer experience. However, as order volumes grow, administrative and tax management can quickly become a bureaucratic nightmare. In Portugal, invoicing is not just a commercial necessity—it is a strict legal obligation regulated in detail by the Portuguese Tax and Customs Authority (AT). This is where the integration between Shopify and Moloni ON becomes your greatest ally.

If you use Shopify, you already know how easy the platform makes it to create and manage a modern e-commerce business. However, as a global platform, Shopify does not issue certified invoices that comply with Portuguese tax legislation. To solve this without spending hours manually transferring data, you need to connect your store to a robust, modern, and fully certified invoicing solution. Moloni ON is the ideal solution to create this bridge automatically and without headaches.

Key takeaways

• Complete automation: Every sale made through Shopify automatically generates a certified invoicing document in Moloni ON, with no manual intervention required.
• Strict legal compliance: Moloni ON is certified by the Portuguese Tax and Customs Authority, ensuring all invoices include the mandatory digital signature, QR Code, and ATCUD.
• Real-time stock synchronisation: Avoid stock shortages or duplicate sales; inventory changes in Shopify are reflected in Moloni ON and vice versa.
• Centralised tax management: Correct VAT configuration for Mainland Portugal, the Autonomous Regions (Azores and Madeira), and international sales (intra-community transactions and exports).
• Simplified SAF-T(PT) export: Generate the monthly tax audit file with a single click, simplifying mandatory communication with the Tax Authority and your accountant's work.

How does the integration between Shopify and Moloni ON work?

The integration between Shopify and Moloni ON operates through a direct API connection or specialised synchronisation applications. Its primary objective is to create a continuous, bidirectional flow of information. Whenever a customer visits your online store, adds products to their basket, and completes a purchase, Shopify records the order and processes the payment. As soon as the order is marked as paid or completed, the data is instantly sent to Moloni ON.

Moloni ON receives customer information (name, Tax Identification Number (TIN), billing address, and email address), product details (unit price, discounts applied, and VAT rates), and shipping information. Based on this data, the system generates the appropriate tax document—which may be an Invoice, Invoice-Receipt, or Cash Sale document—digitally signs it, and adds all legally required elements, including the QR Code and ATCUD. The customer then receives the document directly by email without you needing to click a single button.

What are the advantages of connecting Shopify to Moloni ON?

The biggest advantage of this integration is the elimination of human error and the significant time savings it provides. Imagine having to manually transfer information from 20, 50, or 100 daily Shopify orders into an invoicing system. The risk of entering an incorrect TIN, mismatching product values, or applying the wrong VAT rate would be substantial. With Moloni ON, this manual process disappears completely.

In addition, you gain full visibility over your business. You have access to detailed real-time financial reports, can manage customers and suppliers from a single modern dashboard, and can be confident that your company complies with all current Portuguese tax regulations. Your operation becomes truly scalable: whether you sell one product per day or one thousand, the administrative effort remains exactly the same.

How is VAT managed for online sales with Moloni ON?

Managing Value Added Tax (VAT) in e-commerce can be complex, particularly when selling internationally. Moloni ON simplifies this process by providing flexible and intelligent tax configuration aligned with Portuguese Tax Authority requirements.

When selling to customers in Mainland Portugal, the system automatically applies the standard VAT rate of 23% (or reduced and intermediate rates where applicable). If your customer is located in the Azores or Madeira, Moloni ON is configured to apply the appropriate regional VAT rates.

For international sales within the European Union, the software fully supports the One Stop Shop (OSS) VAT regime. This means that if your sales exceed the legal threshold, Moloni ON can apply the VAT rate applicable in the customer's country. When selling to business customers (B2B) with a valid VAT number verified through the VIES system, the software automatically applies the VAT exemption for intra-community supplies. All of this is handled automatically based on the customer's location and profile within Shopify.

Does Moloni ON automatically issue invoices with QR Codes and ATCUD?

Yes, completely natively and without requiring additional setup from the user. Since the legislation requiring QR Codes and the Unique Document Code (ATCUD) on all tax-relevant documents came into force in Portugal, Moloni ON has ensured full compliance.

As soon as Shopify sends the order data, Moloni ON communicates with the Portuguese Tax Authority through previously registered and validated invoice series, obtains the necessary validation information, and generates the final document. The PDF invoice downloaded or received by your customer already includes a fully compliant QR Code and correctly structured ATCUD. This helps avoid significant penalties and ensures your online store operates entirely within Portuguese legal requirements.

How does stock synchronisation work between the two platforms?

One of the biggest challenges for online retailers is maintaining accurate inventory levels. If you sell the last available item in Shopify, your management system needs to know immediately. Otherwise, you risk selling products that are no longer available. With Moloni ON integration, inventory management is fully automated and bidirectional.

When you add new products or update stock quantities in Moloni ON—for example, after receiving stock from a supplier—those changes are automatically transmitted to Shopify. Likewise, whenever a sale occurs in your online store, stock quantities are automatically deducted from the corresponding product record in Moloni ON. This provides a unified, real-time view of your inventory and current assets at any time.

Which documents should you issue for online sales?

Exporting and submitting the SAF-T (PT) file is one of the most important monthly obligations for businesses and self-employed professionals in Portugal. This XML file contains all invoicing information, credit notes, transport documents, and receipts issued during the previous month and must be submitted through the e-Fatura portal within the legally established deadline.

In Moloni ON, this process is designed to be simple and intuitive. You do not need technical knowledge or database expertise. Simply access the tools and exports section, select the relevant month, and download the SAF-T (PT) file. The file is generated with the correct structure and is ready for validation by the Tax Authority or for submission to your certified accountant. Because Shopify integration ensures all sales are correctly invoiced, your SAF-T (PT) file remains accurate and free from discrepancies.

How to configure your Shopify store with Moloni ON step by step

Para colocares este ecossistema a funcionar, o processo é bastante direto e descomplicado. Segue estes passos essenciais para garantires uma ligação perfeita:

1. Preparing your Moloni ON account

Before configuring Shopify, ensure your Moloni ON account is fully set up. This includes company details, invoicing series already communicated to the Tax Authority, and correctly configured VAT rates.

2. Installing the connector or integration app

Access your Shopify administration panel and visit the App Store. Search for the official connector or a recommended integration application for Moloni ON. Install the application and grant the necessary permissions to access orders and customer data.

3. Authentication and API connection

The application will request your Moloni ON credentials or API key. Enter the required information to establish a secure connection between both platforms.

4. Mapping taxes and payment methods

This step is essential. Match the tax rates configured in Shopify (such as 23% VAT) with the corresponding tax codes in Moloni ON. Do the same for payment methods such as Multibanco References, MB WAY, Credit Cards, and PayPal. This ensures that when invoices are generated, Moloni ON correctly records how payment was received.

5. Activating automation

Define the trigger for document generation. For most online stores, the recommended setup is to automatically issue an Invoice-Receipt as soon as the order status changes to "Paid" in Shopify. Save the configuration and perform a live test to confirm everything works correctly.

Which documents should you issue for online sales?

The correct document depends on your sales and payment workflow.

In e-commerce, the most common scenario is immediate payment during checkout. In these cases, the ideal document to issue automatically through Moloni ON is the Invoice-Receipt.

This document performs two functions simultaneously:

• It serves as proof of the sale (Invoice).
• It confirms that payment has been received in full (Receipt).

If your store offers payment methods where products are shipped before payment is received—such as cash on delivery—you should configure the system to issue an Invoice first. Once payment is received from the carrier or postal service, you can issue the corresponding Receipt through Moloni ON to settle the invoice. If you need to process product returns or customer refunds, the integration also allows you to generate a Credit Note linked to the original invoice, ensuring tax compliance and maintaining accurate accounting records.

This allows your e-commerce operation to remain fully compliant, efficient, and scalable as your business grows.