How to Create an Invoice Series in Moloni

Moloni is one of the most widely used certified invoicing packages in Portugal. Its internal organisation of series is done through Document Sets, a notion that confuses anyone coming from another system but which maps one to one onto the series you file with the tax authority.

This guide covers creating a series in Moloni, filing it, and configuring it correctly for certified issuing with an ATCUD.

What Document Sets are in Moloni

In Moloni a Document Set is what Portuguese law calls a series. Each set groups documents of the same type (invoice, invoice-receipt, credit note and so on) with its own sequential numbering and a unique identifier.

New accounts get default sets (A) created automatically for each document type. That works, but for an online shop or any business with volume it is better to create custom sets reflecting the financial year and the sales channel.

Before creating a set, make sure you have the AT sub-user ready to file series. See ATCUD: creating the user at the tax authority.

Step 1: open set creation

1. Sign in to Moloni.
2. In the top menu go to Definições.
3. Submenu Documentos → Conjuntos de Documentos.
4. The page lists the existing sets. Click Adicionar (top right) to create a new one.

Step 2: configure the new set

The form asks for:

| Field | What to put | Example | |---|---|---| | Name | A unique identifier, capitals and digits. No spaces, no special characters. | 2026FR | | Document type | Pick the type this set applies to from the dropdown | Fatura-Recibo | | Starting number | Usually 1. Migrating from other software, set the next number. | 1 | | Year | The financial year the series starts in | 2026 | | Active | Tick to activate | ✓ |

Some accounts also show:

• Document prefix: text appearing before the number, usually the set name itself.
• Establishment: only if you have more than one configured.
• Default for this type: tick it if this set should be the default when creating a new document of that type.

Important: the Name you put here has to match exactly the series identifier you file with the tax authority. Differences in case, spaces or extra characters make the SAF-T file rejected later on.

Step 3: file the series with the tax authority

From here you have two routes.

Route A: automatic filing from Moloni (recommended)

Moloni integrates directly with the Portal das Finanças. To use it:

1. In Definições → Comunicação AT (or Definições → Configurações da Empresa → Webservice AT), enter the AT sub-user and its password, the NIF/N you created on the Portal das Finanças.
2. In Definições → Documentos → Conjuntos de Documentos, pick the set you just created and click Comunicar Série à AT.
3. Moloni sends the request by webservice. Within seconds the 8-character ATCUD validation code is filled into the set automatically.

Route B: filing by hand on the Portal das Finanças

If you prefer to do it directly:

1. Go to Portal das Finanças → Todos os Serviços → Faturas e Outros Documentos Fiscais → Comunicar Séries Documentais → Registar Série.

2. Fill in:

   • Document type: the same as the Moloni set.
   • Series identifier: the same as the set Name (2026FR).
   • Starting sequence number: the same.
   • Processing method: Programa informático de faturação.
   • Certification number: 2860, Moloni's current number with the tax authority. Always confirm it in the Moloni panel under Sobre, or in the footer of an issued document, in case it changes.

3. Submit. The tax authority returns the validation code.

4. Back in Moloni, edit the set and paste the code into the ATCUD field.

Step 4: make it the default set (optional)

If this is going to be the main set for issuing invoice-receipts from Shopify or Stripe, mark it as default:

1. Definições → Documentos → Conjuntos de Documentos.
2. Click the set.
3. Enable Default for this document type.

Each document type (FT, FR, NC and so on) can have one default set. The others stay active and available for manual selection.

Step 5: verify certified issuing

Before connecting the Shopify or Stripe integration, issue one manual test invoice, which you can void afterwards, and confirm:

• The document shows the identifier <TYPE> <SET-NAME>/<NUMBER>, for example FR 2026FR/00001.
• It carries a QR Code.
• It carries an ATCUD: <code>-<number> line.
• The generated PDF mentions the certified software and its certification number.

If any of these fails, the series is not properly certified.

Common mistakes in Moloni

• A set with no ATCUD: the warning Série não comunicada à AT appears at the top. Go to Definições → Documentos → Conjuntos and file it, by route A or B.
• A set name that does not match: editing is not allowed once the first document is issued. If you got it wrong, create a new set with the right name and deactivate the old one.
• Wrong document type: same again. There is no way to change the type after issuing. Create a new set.
• Skipped numbering: Moloni does not allow manual jumps in the sequence. Rejecting a draft does not consume a number; only finalising the document does.

How Rioko helps

Once the series exists in Moloni with its ATCUD configured, open Rioko, go to the relevant integration page (Stripe + Moloni or Shopify + Moloni) and copy the set's Document Set ID into the Rioko dashboard. You will find the id in Moloni under Definições → Documentos → Conjuntos → <your set> → URL (the number at the end of the URL) or through the API. From there, every invoice Rioko generates automatically from Shopify orders or Stripe payments uses that series, with a valid ATCUD and a QR Code compliant with Portaria 195/2020. If the concept of a series is still new to you, read Invoice series: what they are and how to file them first.

Set up the Stripe + Moloni integration →