How to configure the company's VAT

What is it for?

The PT fiscal configuration window brings together the VAT data the Certified accountant has to confirm for a company: the fiscal region, the VAT regime and periodicity, and whether the company has organised accounting. The periodicity decides the periods of the periodic VAT return, and organised accounting decides whether the returns require a certified accountant. The region decides the regions annex of the periodic return and the rates that an item's heading suggests. The company's default rate does not change with the region: it only changes with the Use regional taxes by default (company's own region) option (see “The company's other VAT options”).

Saving the configuration creates no journal entries: it only changes the company's data.

When to use it?

• In a new company, before preparing the first periodic VAT return.
• When the company changes VAT regime or periodicity, after notifying the Tax and Customs Authority (AT).
• When the certified accountant confirms whether the company is required to have organised accounting.

Where to find it?

Accounting › Configure › VAT and withholding › Tax configuration

The window always opens on the company you are working in (the Company field cannot be changed). To configure another company, switch company in the top right corner and open the menu again.

Before you start

• Certified accountant profile. The Accountant does not see the menu (they only have Entry templates and the bank and asset menus under Configure).
• Have to hand the tax status registered with the AT: VAT regime, start date if it is an exemption regime, periodicity.
• Confirm with the certified accountant whether the company is required to have organised accounting.

How to use it

1. Open Accounting › Configure › VAT and withholding › Tax configuration. The PT fiscal configuration window for the current company opens.
2. In Fiscal region, choose Mainland, Azores or Madeira. The region decides Annex R of the periodic return, but the default rate does not change with it: in the demo, changing the Fiscal region of Empresa Teste Filial from Mainland to Madeira left the default sales and purchase rate at 23%. In a new company the region is suggested from the postal code. For a company in the Azores or Madeira, see the Use regional taxes by default (company's own region) option, under “The company's other VAT options”: that is what changes the default rate.
3. In VAT regime, choose Normal regime, Exempt (CIVA art. 9), Exempt (CIVA art. 53, small business) or Mixed taxpayer (with and without right to deduct). For an exemption regime, fill in VAT regime since with the date it started: without it the window does not save (see “Common problems”). What each regime changes (and what it does not change on invoices) is in How to fill in the company's tax data. The Mixed taxpayer (with and without right to deduct) option is the same choice as the Mixed VAT taxpayer box in the Settings: in the demo, saving the mixed regime here ticked the box, and going back to Normal regime unticked it. With the mixed regime chosen, the window shows the Open the VAT deduction percentage (pro rata) link below, which opens the company's deduction percentage.
4. In VAT periodicity, choose Monthly or Quarterly. If the company already has posted entries this year and you choose another periodicity, a warning appears below: “CIVA art. 41.º: the monthly or quarterly periodicity depends on the turnover of the previous year and on the taxpayer's option. Changing it during the year may not be allowed: check it with your certified accountant.” To save, tick I confirm the change of periodicity during the year, below the warning.
5. In Organized accounting, choose one of the three options: Yes, obliged to have organized accounting, No (simplified regime or exempt) or Not defined. Not defined is the value for a new company: it does not ask for the source and, according to the field's help, it “only warns”. With Yes or No, Source of this answer appears, and it is required: write where the answer comes from, for example Sociedade por quotas; confirmado com o contabilista certificado.
6. Decide on Block submissions without a certified accountant. Unticked (by default), the periodic return of a company with organised accounting and no certified accountant only warns; ticked, validation is refused. It only has an effect with Organized accounting set to Yes. The certified accountant is recorded as described in How to set the responsible certified accountant.
7. Click Save. The window closes and the notification “Saved. VAT periodicity: Monthly.” appears (with the periodicity you chose).

Expected result

• The notification “Saved. VAT periodicity: …” and, when you open the window again, the values you chose.
• The administrator sees the same values on the company record, PT Localization tab (the Certified accountant profile does not have the Settings, where that record is), with the same name VAT periodicity.
• The next periodic VAT return uses the saved periodicity.

Important notes

Periodicity and regime are those registered with the AT

fiscaldoo does not decide the regime or the periodicity: it uses what you save here. The periodicity depends on the previous year's turnover and on the company's option (VAT Code (CIVA), art. 41). Change it only after the certified accountant confirms that the change was accepted by the AT and from which period, and change it only in this window: it is the only place that asks for the art. 41 confirmation. The periodicity also appears in Settings › Billing, VAT (PT) section, VAT region, periodicity and regime block (VAT periodicity), and on the company record, PT Localization tab, with the same name. In a year with posted entries, the Settings and the company record refuse the change: in the demo, changing from Monthly to Quarterly and clicking Save opened Invalid Operation (“A periodicidade do IVA da empresa “Empresa Demonstração, Lda” não se pode mudar aqui. … Como resolver: o Responsável fiscal muda-a em Contabilidade › Configurar › IVA e retenções › Configuração fiscal, que pede a confirmação e deixa a mudança no registo de auditoria.” — the company's VAT periodicity cannot be changed here; the Fiscal officer changes it in the Tax configuration window, which asks for confirmation and records the change in the audit log), and the periodicity stayed Monthly. Pending validation by a certified accountant: when the periodicity can be changed and from which period, and the obligation to have organised accounting (Corporate Income Tax Code (CIRC), art. 123).

• New company: the VAT periodicity is empty, and the window does not save without it (see “Common problems”), except under an exemption regime. In the demo, Empresa Teste Filial with Exempt (CIVA art. 53, small business), VAT regime since 01/01/2026 and an empty periodicity saved with the notification “Saved. The company has no VAT periodicity: it is exempt, so it files no periodic VAT return.” Pending validation by a certified accountant: exemption from the periodic return under each exemption regime (CIVA, art. 9 and art. 53).
• Change log: the help on the VAT regime field says that each change is recorded in the audit log and that the regime is never inferred automatically from the turnover.

The company's other VAT options

The following options are not in this window. They are changed in the Settings and on the company record, which only the administrator can open. The boxes are off by default, except the intra-Community exemption one, which is on; the VAT return cycle and the Tax Calculation Rounding Method are choices, with the default value shown in the table.

Option	Where	What it does
Intra-community exemption needs a valid VIES check	Settings › Billing, VAT (PT) section	It is on by default, and we recommend keeping it that way. What it does for each VIES status, on and off, is in How to create a customer with the right tax data, section “The company's option”. The option is per company: check the company at the top of the screen before clicking Save. Only turn it off if the certified accountant decides so.
Import VAT assessed in the VAT return	Settings › Billing, VAT (PT) section, and company record	Only for a company that has opted, with the AT, to assess import VAT on the periodic return (the screen mentions fields 18 and 19) instead of paying it at customs. The screen says it requires a monthly return.
Mixed VAT taxpayer	Settings › Billing, VAT (PT) section, and company record (VAT DEDUCTION (CIVA ART. 23) group)	It is not a separate option: it is the same choice as the Mixed taxpayer (with and without right to deduct) option of the VAT regime (step 3), and changing one changes the other. It turns on the calculation of the deduction percentage (pro rata).
Apply regional fiscal position by partner's region (goods)	Company record, REGIONAL FISCAL POSITIONS (AZORES/MADEIRA) group	When on, an invoice to a customer with an Azores or Madeira postal code automatically gets the region's fiscal position and rates (in the demo, for a customer in Funchal, Portugal — Madeira and 4% MA). When off (the default), the invoice gets the Mainland rate. The screen's help asks you to check with the certified accountant before turning it on.
Use regional taxes by default (company's own region)	Company record, same group	For a company in the Azores or Madeira: when on, the company's default rate becomes the region's standard rate. Turning it off does not restore the previous rate. Both regional options are explained in How to choose the right VAT rate and know which exemption reason is printed, section “Customers and companies in the Azores and Madeira”.
VAT return cycle	Company record, PT Localization tab	Review, submit and pay (default), Review only (the delivery and the payment are made outside the system) or Payment only (no review step: computed returns can be submitted and paid). It decides which steps of the periodic return are done in fiscaldoo.
Lock the period when the return is submitted	Company record, PT Localization tab	When on, recording the submission of the return closes the VAT period straight away. When off, the period is closed with Close VAT period, on the return.
Proof of export required to close the period	Company record, VAT group	When on, the period's return cannot be validated while there are exports without the proof (the customs document) recorded.
VAT Group regime	Company record, VAT group	For a company that belongs to a VAT group. It asks for the NIF of the dominant entity, and fiscaldoo only accepts the group with the Normal regime and Monthly periodicity: otherwise, on saving, “Validation Error” appears (“… só podem sê-lo empresas no regime normal de IVA com periodicidade mensal (Lei 62/2025, art. 1.º, n.º 7, al. c)) …” — only companies under the normal VAT regime with monthly periodicity can be).
Tax Calculation Rounding Method	Company record, PT Localization tab	Round per Line (default) or Round Globally.

On the company record, the VAT return cycle, Lock the period when the return is submitted and the Tax Calculation Rounding Method are in the VAT group, after Proof of export required to close the period. The same VAT group shows the Recapitulative statement periodicity, which you do not choose: it is calculated and the field's help explains the rule. The statement itself is covered in How to prepare the recapitulative statement. Cash-accounting VAT has its own sign-up button, described in How to fill in the company's tax data.

Left out of the table, because they do not change the VAT of a company that does not use them and are schemes with their own article: the BALCÃO ÚNICO (OSS)…, BALCÃO ÚNICO DAS IMPORTAÇÕES (IOSS)… and REVENDEDORES DE COMBUSTÍVEIS… groups on the company record, only for those who have joined those schemes, and the Cross-check deducted VAT with e-Fatura box in the Settings, which according to the screen's help is “Information only: nothing is blocked”. Pending validation by a certified accountant: the option to assess import VAT on the return (CIVA, art. 27(8)) and the return fields it uses; the VAT groups rule (Lei 62/2025).

Update notice (companies that already existed). The update that made refusal the default turned the option on in every Portuguese company, because there was no record of anyone having changed it by hand. In those companies, the Settings show below the option: “Esta opção foi ligada por uma atualização: a partir de agora uma fatura com a isenção intracomunitária (0 % EU) para um cliente cujo NIF não é válido no VIES é recusada. Não há registo de a opção ter sido mudada à mão, por isso foi ligada em todas as empresas portuguesas; desligue-a aqui se a empresa preferir só o aviso.” (this option was turned on by an update: from now on an invoice with the intra-Community exemption (0 % EU) for a customer whose tax number is not valid in VIES is refused; there is no record of the option having been changed by hand, so it was turned on in every Portuguese company; turn it off here if the company prefers only the warning). Check with the certified accountant whether the company wants it on and click Understood: the notice disappears and the option stays as it is. In a company created after the update, the option is already on and the notice does not appear.

Common problems

“Invalid Operation” appears on saving because of the periodicity

• Message: “Alterar a periodicidade da DP IVA durante o ano exige a sua confirmação. Art. 41.º do CIVA: a periodicidade mensal ou trimestral depende do volume de negócios do ano anterior e da opção do sujeito passivo, pelo que não deve ser alterada a meio do ano sem confirmar com o seu contabilista certificado. Assinale a confirmação para continuar.” (changing the DP IVA periodicity during the year requires your confirmation; tick the confirmation to continue)
• Cause: you chose another periodicity in a year in which the company already has posted entries, and the box below the yellow warning is unticked.
• What is saved: nothing. In the demo, the Fiscal region, Organized accounting and Source of this answer were changed together with the periodicity and, on opening the window again, all the fields were as before: Mainland, Not defined, the source empty and Monthly.
• What to do: click Close on the message. If the certified accountant confirmed the change of periodicity, tick I confirm the change of periodicity during the year and click Save. If not, set the periodicity back to what it was and click Save.

“Invalid Operation” appears on saving: the VAT periodicity is missing

• Message: “Falta a periodicidade do IVA. O que aconteceu: uma empresa portuguesa que liquida IVA entrega a declaração periódica todos os meses ou todos os trimestres (art. 41.º do CIVA) e os períodos e prazos das declarações dependem dela. Nada foi guardado. Como resolver: escolha “Mensal” ou “Trimestral” em “Periodicidade do IVA” e guarde de novo.” (the VAT periodicity is missing; nothing was saved; choose Monthly or Quarterly in VAT periodicity and save again)
• Cause: the VAT periodicity is empty, as in a new company. In the demo, this was the case for Empresa Teste Filial, with the Normal regime.
• What to do: click Close, choose Monthly or Quarterly with the certified accountant (step 4) and click Save.

“Validation Error” appears on saving because the regime date is missing

• Message: “Company "Empresa Demonstração, Lda": the exempt VAT regime needs the date it started ("VAT regime since"), because the DP IVA period depends on it. Fill it in and save again.”
• What to do: fill in VAT regime since and click Save.

“Some required fields are empty” appears on saving

• Message: “Some required fields are empty. Fill in the fields marked in red to be able to save.”
• Cause: you answered Yes or No in Organized accounting and left Source of this answer empty.
• What to do: write the source of the answer and click Save.

I do not see the Tax configuration menu

• Cause: of the values of the Profile field, the menu only appears to the Certified accountant (and to the administrator). The product's message calls it “Fiscal officer”, the name of the access.

• What to do: ask someone with that profile to do the configuration, or ask the administrator to give you the profile. See also I do not see a menu or a button.