Running a Portuguese Company From Abroad: VAT, Invoicing & Cross‑Border Tax Essentials (2025 Guide)

INLIS Consulting
Jul 22
4 min read

If you own a Portuguese company but live primarily outside Portugal (for example, in Singapore), you face a unique triangle of obligations: VAT compliance, digital invoicing rules, and cross‑border tax on profit distributions.

This up‑to‑date 2025 guide brings the moving parts together so you can stay compliant, avoid penalties, and free yourself to focus on growth.

Who is this guide for? International founders, remote directors, holding‑company structures, and globally mobile entrepreneurs

Digital Tax Residence Certificates & Faster Relief

The FASTER (Faster & Safer Tax Relief of Excess Withholding Taxes) Directive is reshaping how investors recover excess tax on cross‑border EU securities income. Why should a private company owner care? Because the Directive’s digital tax residence certificate (eTRC) and standardised relief‑at‑source / quick refund procedures signal where all cross‑border tax admin is heading, including areas adjacent to corporate ownership, portfolio investments, and potentially proof‑of‑residency requests in other tax processes.

What FASTER Does

Introduces a single EU digital tax residence certificate usable across Member States within a calendar year.
Requires Member States to offer relief at source (apply treaty rate up front) or a defined quick refund channel with strict deadlines.
Creates the concept of Certified Financial Intermediaries who report and help validate investor eligibility.
Aims to reduce fraud exposed in Cum‑Ex/Cum‑Cum cases and cut hundreds of local language forms now clogging refund claims.

Timeline

Political agreement reached 14 May 2024; formally adopted 10 Dec 2024; Member States must transpose; full operational go‑live targeted for 1 Jan 2030 (subject to national implementation). Start collecting clean beneficial ownership data now—future bank/broker processes will demand it.

VAT vs. Withholding Tax: Don’t Confuse Them

Because both hit cross‑border transactions, they’re often mixed up:

Feature	VAT	Withholding Tax
Nature	Consumption tax on goods/services	Tax on income payments (dividends, interest, royalties)
Who Bears the Cost	End consumer (economically)	Income recipient
Credit/Recovery	Input VAT deduction & refunds	Treaty rate reduction or foreign tax credit
Admin Channel	Invoicing & periodic returns	Applied at payment, relief via forms, or relief‑at‑source
Digital Evolution	ATCUD, QR, e‑invoicing, SAF‑T	eTRC, Certified Intermediaries (FASTER)

Understanding the difference helps avoid misclassifying cross‑border charges and missing reclaim opportunities.

Remote Owner Compliance Checklist (Before, During & After Trips to Portugal)

Before You Travel to Portugal

Confirm Portuguese VAT registration status (active? correct regime?).
Verify the fiscal representative mandate & contact details are current.
Ensure the invoicing system generates ATCUD & QR and maps the correct VAT rates.
Review pending VAT returns & payment balances.
Download the latest SAF‑T PT export; backup in a secure cloud.

While in Portugal (Good Governance)

Hold at least one board/management meeting in Lisbon; minute location for substance.
Review physical operations vs. reported establishment (e.g., warehouse, staff, contractors).
Spot‑check sample invoices for the correct VAT rate and ATCUD display.
Meet bank, accountant, and fiscal rep; align on upcoming QES 2026 changes.

After You Return Abroad

Approve VAT filings remotely (digital signature workflows).
Reconcile input VAT on trip expenses (lodging, transport, professional meetings).
Plan profit distribution calendar; gather residency certificates for treaty WHT.
Update management control evidence (board resolutions, signatory records) to support the corporate tax residency position if challenged.

How INLIS Consulting Supports International Business Owners

We work with globally mobile founders who need a single point of contact in Portugal.

Our English‑speaking accounting & tax team can:

Assess whether you must register or deregister for VAT; file applications.
Configure or fully manage AT‑certified invoicing software (ATCUD, QR, multi‑currency, English docs).
Monitor VAT deadlines; prepare & submit monthly/quarterly returns; manage payments.
Produce & validate SAF‑T PT billing/accounting files; archive audit‑ready ledgers.
Prepare for QES 2026 electronic signature requirements.
Analyse cross‑border dividend & interest flows (Portugal → Singapore/Malta/elsewhere) and coordinate treaty relief paperwork.
Advise on corporate tax strategy amid Portugal’s evolving CIT landscape.

Let us be your Portugal back‑office so you can run the business from anywhere.

Frequently Asked Questions

Do I need to charge Portuguese VAT if all my clients are outside Portugal?

Maybe not, but if your business has a Portuguese establishment incurring input VAT, voluntary registration may allow recovery. Cross‑border B2B vs. B2C rules differ; get advice.

I’m below €15k turnover— should I stay in the exemption?

If you incur material Portuguese costs with VAT, opting into VAT can improve cash flow through input recovery. Model both scenarios.

What happens if I forget to file a quarterly VAT return ?

Expect fines, interest, and growing audit risk. Repeated failures can impact refund claims and your fiscal representative relationship.

Can my cloud accounting platform outside Portugal issue compliant invoices?

Only if it’s AT‑certified or integrates with a certified Portuguese layer that adds ATCUD/QR and exports SAF‑T files.

Do I need a Portuguese digital certificate to sign invoices?

From 1 Jan 2026, PDF invoice flows will require a Qualified Electronic Signature; we can provision this.

How do I avoid double taxation when taking dividends to Singapore?

Use the Portugal–Singapore treaty rate (typically max 10%) and claim foreign tax credits; collect residency evidence and apply timely.

Does the EU FASTER Directive affect private companies?

Indirectly, for now, it targets portfolio securities, but its digital residency and standardisation themes are spreading across tax processes. Expect knock‑on effects.