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Cairos for clinics and practices

Invoicing for clinics and healthcare practices

Healthcare is exempt from VAT, but aesthetic treatment is not, and neither is an expert report. As soon as the two live side by side the prorrata appears, and that is where a small practice starts deducting the VAT on everything else wrongly.

Exempt and taxable kept apartProrrata worked out and adjustedHealth data protected
erp.cairos.es
General
Dashboard
Invoices
Quotes
Contacts
Expenses
Products
Accounting
8.940 €
Invoiced this month
7.180 €
Exempt from VAT
1.760 €
Subject to VAT
20 %
Provisional pro rata
F-2026/0318Physiotherapy session45,00 €Exempt
F-2026/0317Aesthetic treatment242,00 €VAT 21%
F-2026/0316Expert report · insurer363,00 €VAT 21%
F-2026/031510-session pass400,00 €Exempt
What changes

What is particular about invoicing in clinics and practices

No other sector on this site has an exemption as broad, or a consequence as tangled as the one it brings.

Healthcare is exempt

Article 20.Uno.3º of the VAT Act exempts care given to natural persons by medical or healthcare professionals — including qualified psychologists, speech therapists and opticians — whoever pays for it. What marks out the exemption is not the recipient but the purpose: preventing, diagnosing or treating illness. Your invoice to the patient goes without VAT, and that is not an option: it is an exemption.

But not everything you do is

Aesthetic medicine with no therapeutic purpose, expert reports, certificates for evidential purposes and product sales do carry VAT. And watch out for the easy argument: they are not taxable «because an insurer pays for them», but because they do not seek to prevent, diagnose or treat. Living with exempt and taxable transactions at once is the norm in a clinic, not the exception.

And that means prorrata

You do not deduct all the VAT on your expenses: only a percentage. During the year you apply the previous year's final percentage, and in the last return of the year you work out the final one with your real income and adjust it all at once. The result is always rounded up. It is the calculation most often got wrong in a practice.

Health data, a special category

A patient's name tied to a treatment is health data, with the reinforced protection of the European Regulation. In an invoicing program the prudent thing is not to put more than necessary in the invoice item.

Day to day

How it is done today, and how it looks with Cairos

In a practice the mess is not in the invoicing: it is in the VAT you have not deducted properly.

Day-to-day work in clinics and practices

Without Cairos

  • Everything is invoiced the same way, without separating the exempt from the taxable.
  • Nobody has heard of the prorrata until an inspection turns up.
  • The VAT on the electricity, the rent and the materials is deducted in full.
  • The invoice items describe the treatment in more detail than is necessary.
  • The insurers pay at their own pace and nobody keeps track.

With Cairos

  • Each service is marked as exempt or taxable from its own record.
  • During the year the previous year's final prorrata is applied, which is what the law requires.
  • In the last return of the year the final one is worked out and adjusted.
  • The item on the invoice says just enough and the clinical detail stays out.
  • Due dates by insurer and by patient are in plain sight.
Taxes

What is exempt and what is not

The exemption covers care given to natural persons with the purpose of prevention, diagnosis or treatment. Anything that does not fit there carries VAT.

ServiceVATWhy
Medical consultation, physiotherapy, psychologyExemptHealthcare under art. 20.Uno.3º, given by a professional with a recognised qualification.
Dentistry and dental prosthesesExemptIt also has an exemption of its own, in art. 20.Uno.5º, which covers the supply and fitting of the prosthesis as well.
Rehabilitation after an injuryExemptIt has a therapeutic purpose.
Aesthetic medicine with no therapeutic purpose21 %There is no prevention, diagnosis or treatment of an illness.
An expert report or a certificate for evidential purposes21 %What takes it out of the exemption is the purpose, not who pays for it: the law says «cualquiera que sea la persona destinataria», whoever the recipient is.
Sale of cosmetics and over-the-counter product21 %It is a supply of goods, and no list in art. 91 covers it.
Medical products on the list in the Act's eighth annex10 %Art. 91.Uno.1.6º.c: medical equipment and apparatus designed to relieve or treat impairments, with its closed list. It is worth looking at it before invoicing at 21%.
Medicines for human use, prostheses and orthoses for people with disabilities4 %Art. 91.Dos.1.3º and 5º. Disability is evidenced with a degree of 33% or more.
Renting a consulting room to another professional21 %It is a lease of business premises, outside the exemption in art. 20.Uno.23º.
Teaching given by the healthcare professionalExempt or taxableIt goes under the education exemption, which is a different one and has its own requirements.

The exemption is set by the purpose of the service and the qualification of whoever provides it, not by the sign on the door or by who signs the cheque. And a clinic with aesthetic treatments or product sales is, almost certainly, on prorrata.

The modelos you end up filing

FormWhenWhy in your case
303QuarterlyOnly for the taxable part, and with the prorrata applied to the input VAT.
390JanuaryThe annual summary, with the final prorrata.
130QuarterlyIf you are an autónomo and less than 70% of your income carries withholding.
111QuarterlyWithholdings for staff and for other professionals.
115QuarterlyThe withholding on the rent for the practice.

Try it with your practice's invoices

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Questions from clinics and practices

Healthcare given to natural persons by professionals with a recognised qualification is exempt, whether the patient, an insurer or a company pays: the law says expressly «cualquiera que sea la persona destinataria», whoever the recipient is. What falls outside the exemption is aesthetic work with no therapeutic purpose, reports for evidential purposes and selling product.
If you have exempt and taxable income, you cannot deduct all the VAT on your expenses: only the percentage that transactions carrying a right to deduct represent of your total transactions, rounded up. During the year you apply last year's final percentage, and in the last return of the year you work out the final one and adjust.
The general one is the default: a single percentage for all your input VAT. The special one deducts 100% of the VAT on whatever you use only in the taxable part, deducts nothing on whatever you use only in the exempt part, and applies the percentage only to shared expenses. You can opt for it on the last return of the year — and it then binds you for three years — and it is also compulsory when the general one would let you deduct 10% more, or more, than the special one would.
Yes, if it is a capital good: those with an acquisition value of €3,005.06 or more are adjusted over the four years following the year of purchase — nine if it is a property — when the prorrata changes. And it is only touched if the difference from the prorrata in the year of purchase is more than ten points. Below that, nothing is adjusted.
Yes: it comes out of your own income, it is applied to your input VAT and it is adjusted when the year closes, with the capital goods table kept separately. It is exactly the point where a spreadsheet breaks.
No. Cairos is invoicing, accounting and taxes; the clinical records and the diary you carry on keeping in your healthcare program. We say so plainly because it is the first question.
As contacts, with their tax details, and nothing more. The recommendation is not to describe the treatment in the invoice item beyond what is necessary: health data has reinforced protection. More detail in security and data.

Your practice invoices differently. So does the program.

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