Complete guide to electronic invoicing for psychologists in Portugal: e-Fatura, ATCUD, VAT exemption, invoicing series, and how to automate the entire process.

Electronic Invoicing for Psychologists: e-Fatura and ATCUD

Electronic invoicing in Portugal has become increasingly demanding and regulated. For psychologists in private practice, understanding tax obligations — from ATCUD to invoice reporting via e-Fatura — is essential to avoid fines and keep your practice legally compliant. This guide covers in detail all aspects of electronic invoicing relevant to psychology professionals in Portugal.

1. Mandatory Electronic Invoicing in Portugal

Portuguese legislation has been progressively strengthening electronic invoicing requirements. The legal framework is based on several key pieces of legislation:

Applicable Legislation

Decree-Law No. 28/2019, of February 15: Establishes the rules for electronic invoicing, including the mandatory use of invoicing software certified by the Tax and Customs Authority (AT).
VAT Code (CIVA): Defines invoice issuance obligations and exemption regimes.
Ordinance No. 363/2010: Regulates the technical requirements for invoicing software.
Law No. 119/2019: Introduced ATCUD as a mandatory element on invoices.

Who Is Required to Comply?

All VAT-registered taxpayers carrying out economic activity in Portugal are required to issue invoices. This includes psychologists working as self-employed professionals ("recibos verdes") or operating through a sole proprietorship.

Since January 1, 2024, the use of AT-certified invoicing software is mandatory for all taxpayers with a turnover greater than zero euros in the previous year — meaning virtually all active professionals. The exception applies only to those who did not issue any invoices in the previous year and are not required to maintain organized accounting.

Issuance Deadlines

Invoices must be issued:

At the time the service is provided or, at the latest, by the 5th working day of the following month.
For psychologists, this means the invoice for each session should be issued on the same day or in the immediately following days.

Practical example: If you conduct a psychotherapy session on Monday the 3rd, the invoice must be issued by Friday the 7th (assuming no public holidays).

2. What Is ATCUD and Why Is It Mandatory

ATCUD (Unique Document Code) is a unique alphanumeric code that must appear on all invoices and fiscally relevant documents issued by taxpayers in Portugal.

How It Works

The ATCUD is composed of two parts:

Series validation code: Assigned by the AT when an invoicing series is registered.
Sequential document number: Automatically generated by the invoicing software.

The format is: ATCUD:XXXXXXXX-NNNNN, where XXXXXXXX is the series validation code and NNNNN is the sequential number.

Example: ATCUD:A4B5C6D7-00001 on a first invoice of the series.

Mandatory Requirement

ATCUD became mandatory from January 1, 2024 for all fiscally relevant documents, including:

Invoices and simplified invoices.
Invoice-receipts.
Credit notes and debit notes.
Receipts.

How to Obtain ATCUD

To generate the ATCUD, you need to:

Register one or more invoicing series on the Finance Portal (or via AT webservice).
Obtain the validation code for each series.
The certified invoicing software automatically generates the ATCUD on each document.

Important note: The ATCUD must be presented both in readable format and as a QR code on the invoice. The QR code contains tax information that allows the AT to validate the document.

Penalties

Failure to include the ATCUD on invoices constitutes a tax offense, subject to fines ranging from 375 to 18,750 euros, under the General Regime of Tax Offenses (RGIT).

3. What Is e-Fatura and How It Works

e-Fatura is the Tax Authority's system that allows taxpayers to view and verify invoices issued in their name, classify them by expense category, and benefit from tax deductions on their income tax (IRS).

For the Psychologist (Issuer)

As a professional issuing invoices, e-Fatura involves:

Reporting invoices to the AT: All issued invoices must be reported to the AT by the 5th of the month following issuance. This can be done via:
- SAF-T (PT) file: Exported by the invoicing software and submitted on the Finance Portal.
- Webservice: Automatic real-time communication (the most efficient method).
- Manual entry: Entering each invoice's data on the Finance Portal (only for those who issue very few invoices).
Monthly SAF-T file: In addition to invoice reporting, it is mandatory to submit the monthly SAF-T (Standard Audit File for Tax Purposes) invoicing file.

For the Patient (Purchaser)

Psychology invoices automatically appear in the patient's personal e-Fatura area, under the Health category. This allows the patient to:

Deduct health expenses on their income tax (15% of health expenses, with a limit of 1,000 euros).
Verify that all invoices have been correctly reported.

Automatic Categorization

When the psychologist is registered with the correct CAE (86906 — Other human health activities, n.e.c.) and issues VAT-exempt invoices under Article 9 of the CIVA, invoices are automatically classified as health expenses in the patient's e-Fatura.

Important tip: Make sure your primary CAE is correctly registered with the Tax Authority. If you have multiple CAEs (for example, one for clinical psychology and another for training), invoices for secondary activities may require manual classification by the patient.

4. VAT in Psychology: Exemption Under Article 9 of the CIVA

One of the most relevant — and frequently misunderstood — aspects of invoicing for psychologists is the VAT regime.

The Exemption

Article 9, No. 1, Paragraph 1) of the VAT Code (CIVA) exempts from VAT the provision of services performed in the exercise of medical, dental, midwifery, nursing, and other paramedical professions. Clinical psychology is covered by this exemption, provided that:

The professional is registered with the Portuguese Order of Psychologists (OPP).
The services provided are clinical psychology acts (therapy, psychological assessment, follow-up consultations).

What Is Exempt

Individual, couples, or group psychotherapy sessions.
Clinical psychological assessment.
Follow-up and psychological support consultations.
Clinical reports issued in the context of therapeutic support.

What Is NOT Exempt (Subject to 23% VAT)

Training and workshops (even on psychology topics).
Organizational consulting and human resources.
Paid lectures and conferences.
Clinical supervision (when provided as an independent service, the situation may vary — consult your accountant).
Coaching (not considered a health act).

Required Invoice Notation

VAT-exempt invoices must include the mandatory legal reference to the exemption:

"VAT — Exempt under Article 9, No. 1, Paragraph 1) of the CIVA"

Invoice example:

Field	Value
Issuer	Dr. Maria Silva, Clinical Psychologist, OPP No. 12345
Issuer Tax ID	234 567 890
Purchaser	Joao Santos
Purchaser Tax ID	210 987 654
Description	Individual psychotherapy session (50 min)
Amount	65.00 EUR
VAT	Exempt — Art. 9, No. 1, Par. 1), CIVA
Total	65.00 EUR
ATCUD	ATCUD:A1B2C3D4-00042
Date	2026-02-19

VAT Regime: Classification

Psychologists who exclusively provide exempt clinical acts fall under the Article 9 exemption regime. This means that:

They do not charge VAT on invoices.
They cannot deduct VAT paid on professional expenses.
They do not file periodic VAT returns.

If they additionally provide VAT-taxable services (training, consulting), they may need to register under the standard VAT regime for those activities, while maintaining the exemption for clinical acts. This situation requires careful accounting oversight.

5. Green Receipts vs. Certified Invoicing Software

This is one of the most common questions among psychologists starting private practice.

Green Receipts (Finance Portal)

Electronic green receipts issued directly on the Finance Portal are a free invoicing option. They allow the issuance of invoice-receipts and are suitable for professionals with low invoicing volume.

Advantages:

Free of charge.
Automatic reporting to the AT.
ATCUD generated automatically.
Suitable for those who issue few invoices.

Disadvantages:

Manual process: each invoice must be issued individually on the portal.
No automation: does not integrate with scheduling or management systems.
No financial reports.
No payment management.
Impractical interface for high volumes.

Certified Invoicing Software

For professionals with regular practice (more than 10-15 sessions per week), AT-certified invoicing software offers significant advantages.

Advantages:

Automated invoice issuance.
Integration with scheduling and clinical management systems.
Automatic reporting to the AT via SAF-T or webservice.
ATCUD and invoicing series management.
Detailed financial reports.
Payment and collection tracking.

Mandatory requirement: Since 2024, certified invoicing software is mandatory for all taxpayers with turnover greater than zero euros, with very limited exceptions. In practice, any psychologist in regular activity should use certified software.

Which to Choose?

If you conduct more than 5-10 sessions per week, certified invoicing software integrated with clinical management is clearly the best option. It saves time, reduces errors, and ensures tax compliance.

6. Legal Requirements: Invoicing Series and AT Reporting

Invoicing Series

Each taxpayer must register their invoicing series with the AT. An invoicing series identifies the numerical sequence of documents.

Rules:

Each document type (invoice, credit note, receipt) must have its own series.
Series must be registered on the Finance Portal before issuing documents.
Each series has a validation code assigned by the AT, used in generating the ATCUD.
Numbering within each series is sequential and cannot have gaps.

Example of series for a psychologist:

FT 2026/ — Invoice series for 2026.
NC 2026/ — Credit note series for 2026.
RC 2026/ — Receipt series for 2026.

Invoice Reporting to the AT

Invoices must be reported to the AT through one of the following methods:

Via webservice (real-time): The software sends each invoice to the AT at the time of issuance. This is the most efficient and recommended method.
Via SAF-T file: Monthly export of the SAF-T file and submission on the Finance Portal by the 5th of the following month.
Via manual entry: Entering each invoice's data on the Finance Portal (only for very low volumes).

SAF-T File

The SAF-T (Standard Audit File for Tax Purposes) is a standardized XML file containing all invoicing information. Monthly submission to the AT is mandatory.

Obligations:

Monthly submission by the 5th of the following month.
The file must contain all invoices issued in the period.
It must include information about cancellations and credit notes.

7. How Mena.ai Automates Invoicing for Psychologists

Mena.ai offers an integrated invoicing solution specifically designed for mental health professionals in Portugal.

AT-Certified Invoicing

Mena.ai's invoicing module is certified by the Tax Authority, meeting all legal requirements:

Automatic ATCUD: The unique document code is automatically generated on each invoice.
Invoicing series: Automatic series management, with prior registration at the AT.
AT reporting: Invoices are automatically reported via webservice, in real time.
SAF-T: Automatic monthly SAF-T file export.
QR Code: All invoices include the mandatory QR Code with tax information.

Simple Setup

The initial setup is guided step by step:

Enter your tax details (Tax ID, fiscal address, CAE).
Configure the applicable VAT exemption (Article 9 of the CIVA).
Register the invoicing series (Mena.ai can do this automatically via AT integration).
Define your services and prices.
Start invoicing — manually or automatically.

Automatic Issuance After Sessions

The most powerful feature is automatic invoicing linked to the schedule. When a session is marked as completed, Mena.ai can:

Automatically generate the invoice with the patient's details.
Apply the correct VAT exemption.
Send the invoice by email to the patient.
Report the invoice to the AT in real time.

8. Schedule Integration: Automatic Invoicing After Each Session

The integration between the clinical schedule and the invoicing system is what distinguishes a truly efficient solution.

Automated Workflow

Appointment booking: The patient books or is scheduled for a session.
Attendance record: At the end of the session, the psychologist marks the appointment as completed.
Automatic issuance: The invoice is automatically generated with the correct details.
Sent to patient: The invoice is sent by email or made available in the patient portal.
AT reporting: The invoice is automatically reported to the Tax Authority.
Payment record: Payment is recorded (manually or automatically, depending on the method).

Exception Management

The system also handles special situations:

Cancelled sessions: No invoice issued.
Price changes: Application of differentiated price tables (for example, social pricing).
Session packages: Invoicing for the complete package or per individual session.
Insurance agreements: Invoicing with the data and formats required by each insurer.

Time Savings

A psychologist conducting 20 sessions per week who spends 3 minutes manually issuing each invoice spends over 50 hours per year on invoicing alone. With automation, that time is reduced to practically zero.

9. Financial Reports and Tax Management

Mena.ai's clinical management includes financial reports that help with tax organization throughout the year.

Available Reports

Monthly invoicing summary: Total invoiced, number of sessions, average per session.
Analysis by service type: Revenue by consultation type (individual, couples, group, assessment).
Payment tracking: Paid, pending, and overdue invoices.
Export for accountant: Files in formats compatible with major accounting software.

Income Tax Preparation

At the beginning of each year, income tax return preparation is simplified:

Annual gross income: Automatically calculated from issued invoices.
Professional expenses: If you use Mena.ai as a professional expense, the invoice is deductible.
Withholding tax: Tracking of withholdings made (when applicable — for example, for services provided to companies).

Simplified Regime: The Calculation

For psychologists under the simplified regime, taxable income is calculated as follows:

Annual gross income: Example — 48,000 euros.
Coefficient: 0.75 (liberal professions under the simplified regime).
Taxable income: 48,000 x 0.75 = 36,000 euros.
Possible reduction: If documented expenses (with invoice and Tax ID) exceed 15% of gross income (7,200 euros in this example), the effective coefficient can be reduced.

Note: The expense deduction under the simplified regime works as follows — if you do not document at least 15% of your income in expenses with your Tax ID, the difference is added to taxable income. In other words, it is essential to keep all invoices for professional expenses.

Social Security

Social Security contributions for self-employed workers are calculated on 70% of the relevant income:

Contribution rate: 21.4%.
Assessment base: 70% of gross income.
Example: With 48,000 euros annually, the base is 33,600 euros, and the annual contribution is 7,190.40 euros (598.20 euros/month).

Mena.ai facilitates this calculation by providing the updated annual gross income in real time.

10. Common Invoicing Mistakes and How to Avoid Them

Mistake 1: Not Including the Patient's Tax ID

All invoices must include the purchaser's (patient's) Tax ID. Without the Tax ID, the patient cannot deduct the expense on their income tax, and the invoice may not be accepted by the AT.

Solution: Request the Tax ID at the first consultation and record it in the management system.

Mistake 2: Incorrect VAT Exemption Reference

Using the wrong reference (for example, citing Article 53 instead of Article 9) can cause tax problems.

Solution: The correct reference for clinical psychology acts is: "VAT — Exempt under Article 9, No. 1, Paragraph 1) of the CIVA". Article 53 applies to the exemption regime for low turnover, which is different.

Mistake 3: Late Reporting to the AT

Invoice reporting to the AT has a legal deadline. Non-compliance can result in fines.

Solution: Use software that reports automatically in real time, or ensure you submit the SAF-T by the 5th of each month.

Mistake 4: Invoicing with the Wrong CAE

If the registered CAE does not correspond to the activity actually performed, invoices may be incorrectly classified in the patient's e-Fatura.

Solution: Check your CAE on the Finance Portal. For clinical psychology, the correct CAE is 86906.

Mistake 5: Not Issuing a Credit Note in Case of Error

If you issued an invoice with an error, you cannot simply cancel it. You must issue a credit note that fully or partially reverses the original invoice.

Solution: Always issue a credit note referencing the original invoice. Never alter or delete invoices already reported to the AT.

Mistake 6: Mixing Exempt and Non-Exempt Activities

Psychologists who also provide training or consulting must clearly separate exempt activities from those subject to VAT.

Solution: Use separate invoicing series for clinical activities (exempt) and non-clinical activities (with VAT). Maintain clear records and inform your accountant.

Mistake 7: Not Keeping Backups

The law requires the retention of invoicing records for 10 years. A computer failure can mean the loss of essential data.

Solution: Use software with cloud storage and automatic backups. Mena.ai ensures the secure retention of all tax documents.

11. Frequently Asked Questions (FAQ)

I'm a psychologist and I only do therapy. Do I need to register for VAT?

If you exclusively provide clinical psychology acts (exempt under Article 9 of the CIVA), you are VAT-exempt and do not need to file periodic VAT returns. However, you must be registered with the Tax Authority as a taxpayer and issue invoices with the exemption reference.

Can I deduct office expenses on my income tax?

Under the simplified regime, you do not deduct expenses directly, but you need to document at least 15% of gross income in expenses with a Tax ID (including personal and professional expenses) to avoid a penalty on the coefficient. Under organized accounting, all documented professional expenses are deductible.

How long do I have to issue the invoice?

The invoice must be issued at the time the service is provided or, at the latest, by the 5th working day of the following month. In practice, issuing it on the same day as the session is recommended.

Can my patients deduct psychology sessions on their income tax?

Yes. Psychology consultations are considered health expenses and are deductible at 15%, with a global limit of 1,000 euros for health expenses. For this, the invoice must contain the patient's Tax ID and be correctly reported on e-Fatura.

If I provide training in addition to clinical practice, how should I invoice?

Training is not VAT-exempt. If your turnover from VAT-taxable activities exceeds 14,500 euros annually (Article 53 threshold), you must charge 23% VAT on those invoices. It is recommended to use separate invoicing series and consult an accountant to manage the mixed regime.

What happens if I don't report invoices to the AT?

Failure to comply with the invoice reporting obligation is punishable with fines ranging from 200 to 10,000 euros, under the RGIT. Additionally, your patients will not see the invoices on e-Fatura, losing the tax benefit.

Do I need a certified accountant?

Under the simplified regime, it is not mandatory but highly recommended. Under organized accounting (mandatory above 200,000 euros in turnover or by choice), it is mandatory to have a certified accountant registered with the Order of Certified Accountants.

What is the SAF-T file and when should I submit it?

SAF-T is a standardized XML file containing all invoicing information. It must be submitted monthly to the AT by the 5th of the following month. Certified invoicing software exports this file automatically.

Can I cancel an invoice that has already been issued?

You cannot simply delete an invoice. You must issue a credit note that fully or partially reverses the original invoice. The credit note must reference the invoice being cancelled and be reported to the AT.

What is the difference between Article 9 and Article 53 of the CIVA?

Article 9 exempts certain activities from VAT based on their nature (health, education, social services). The exemption applies regardless of turnover. Article 53 exempts taxpayers with annual turnover below 14,500 euros from VAT, regardless of the activity. A clinical psychologist benefits from the Article 9 exemption for clinical acts; Article 53 may be relevant for other activities (training, consulting) if the volume of those activities is low.

12. Conclusion

Electronic invoicing in Portugal is an unavoidable reality for any psychologist in private practice. With mandatory ATCUD, invoice reporting to the AT, and the growing demands of e-Fatura, tax compliance requires attention and the right tools.

Key takeaways:

Use certified invoicing software — it is mandatory and saves you time.
Always include ATCUD and QR Code on invoices.
Correctly apply the VAT exemption (Article 9 of the CIVA for clinical acts).
Report invoices to the AT within legal deadlines.
Keep records for 10 years.
Separate exempt from non-exempt activities if you provide diversified services.

Mena.ai's automated invoicing was designed to eliminate the tax complexity of clinical practice. From automatic invoice issuance with ATCUD to real-time reporting to the AT, every detail was thought out so that psychologists can focus on what truly matters: their patients.

Tax compliance does not need to be a burden. With the right tools, invoicing becomes invisible — and your time is freed for clinical practice.