Accounting for doctors and clinics in Porto.

Accounting for doctors and clinics in Porto

Who is it for?

Self-employed doctors and dentists, doctors who combine hospital work with private practice, medical practices, clinics and surgeries, and other healthcare professionals — psychologists, nurses, physiotherapists and therapists. We are based in Porto, with clients throughout the country.

VAT: exempt, but not entirely

Services provided in the course of practising as a doctor, dentist, psychologist, nurse or in other paramedical professions are exempt from VAT (Article 9(1) of the VAT Code). This exemption does not give rise to a right to deduct: VAT paid on equipment, building works and rent is not recoverable.

A doctor, acting in a personal capacity, may not waive this exemption. The option to waive the exemption applies to clinics and other healthcare establishments (Article 9(2)), for services not provided under agreements with the State within the framework of the National Health Service, and requires them to remain in the chosen scheme for at least five years (Article 12). A comparison is made between the VAT that the clinic will now charge and the VAT it will recover on its investment — and the decision is based on the figures. We explain the rule in detail in the article on the waiver of VAT exemption for clinics.

The exemption covers healthcare. Non-therapeutic procedures — such as certain cosmetic procedures — and the sale of products are subject to tax, and where the same person or clinic carries out both exempt and taxable transactions, the VAT that can be deducted must be separated.

Income Tax for self-employed workers: simplified scheme or organised accounting

Medicine is included in the list of activities set out in Article 151 of the Personal Income Tax Code. Under the simplified scheme, which applies to annual income of up to €200,000, personal income tax is payable on 75% of the invoiced amount. However, there is one condition: 15% of the invoiced amount must be supported by business expenses — rent, wages, invoices submitted via e-fatura, social security contributions — and any shortfall is added to the income (Article 31(13)).

With proper bookkeeping, you pay tax on actual profit: it’s worth it when expenses exceed 25% of turnover, which is the case if you have your own practice, assistants or expensive equipment. You can compare the two schemes using the simplified tax regime simulator or organised accounting.

Where the client is a clinic or hospital with a properly organised accounting system, receipts are subject to a 23% withholding tax. Those who expect to invoice less than €15,000 per year may apply for an exemption from withholding tax.

Hospital treatment and private consultations in the same year

Income from hospital employment (category A) and self-employment (category B) are combined on the same income tax return and taxed at the same rates. The reduction in the tax coefficient during the first two years of self-employment does not apply to those who also receive a salary, and social security contributions on self-employment income may be exempt when combined with employment income, within certain income limits. Before starting your business, we calculate your final income tax — you can run a simulation on the Income Tax simulator.

Medical associations and tax transparency

A partnership in which all partners are doctors, formed for the purpose of practising medicine, is a professional partnership and is subject to the tax transparency regime (Article 6 of the Corporation Tax Code): it does not pay corporation tax, and the profit is allocated to the partners, who declare it on their personal income tax returns — even if it is not distributed. A company with partners who are not doctors, or a clinic engaged in other activities, is subject to corporation tax in the same way as any other company. Further details can be found in the article on fiscal transparency.

Working as a sole trader, in a professional partnership or in a clinic registered for corporation tax yields very different results depending on your income, what you wish to take out of the business and the level of investment. We work this out before setting up the company.

Patient data

The SAF-T invoicing file contains the name and tax identification number of each patient. We only request the information required for your accounts, and the documents are stored in our client area, with access restricted to those responsible for your accounts.

How we work

1. Background. We can see what we’re invoicing today, to whom, and what the expenses are — and we choose the VAT, personal income tax (IRS) or corporation tax (IRC) and social security schemes.
2. Every month. Please submit your invoices and statements via the customer portal; we’ll post them, reconcile them and take care of the tax returns.
3. At the end of the year. IRS or Form 22 and IES, with the calculations completed before submission.

The accounts and tax returns are signed by a Certified Accountant registered with the Institute of Certified Accountants (see Legal information). The rules described here are those for 2026; the classification of each case is always confirmed at the first meeting.

Frequently asked questions

Do doctors have to charge VAT on consultations?

No. Healthcare provided by doctors is exempt from VAT. Services not provided for therapeutic purposes and the sale of goods are subject to VAT.

Can I claim back the VAT on the equipment for my surgery?

Not as a sole trader: the exemption does not entitle the business to a deduction. A clinic that opts out of the exemption will then charge VAT and reclaim what it pays, and is obliged to remain under that regime for at least five years.

Is it worth setting up a company?

It depends on the income, the expenses and what you want to take out of the partnership. A partnership made up solely of doctors is subject to fiscal transparency, and the profit is taxed as part of the partners’ personal income tax; that’s why we work out the figures before making a decision.

Which expenses count towards the 15% under the simplified scheme?

Social Security contributions (or the specific deduction, whichever is higher), salaries paid, rent for the surgery, invoices relating to the business reported via e-fatura and, if the surgery is owned by you, 1.5% of the asset value.

Do you work with clinics outside Porto?

Yes. Documents are sent via the client portal and meetings can be held via video call.

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