Switching clinic management software without losing patient data

Switching clinic management software without losing patient data takes five steps: take an inventory of what you have, ask your current provider for a complete export, clean the files, test the import with a copy, and let the two programs run side by side for a few weeks. Whatever cannot be brought into the new program, such as old medical records or signed documents, is not deleted: it is kept and stays easy to find. And before loading the first patient, sign the processing contract with the new provider.

Step 1: take an inventory of what you have

Before talking about files, list what data the clinic holds and where it lives. There are usually more places than you think: the current program, a diary in another application, paper consent forms, photos on a computer in the consulting room. For each type of data, decide what you want to do with it:

Data	Usual decision
Patients (identification and contact details)	Migrate. It is the first thing you need in order to work.
Future appointments	Migrate, or rebook them in the new program from the cut-over date.
Past appointments	Migrate if the new program allows it; they give context but are not urgent.
Medical records	Depends on what both programs can export and import. If they are not migrated, archive them so they can still be consulted.
Consent forms and signed documents	Keep them exactly as signed, normally as PDF or on paper.
Clinical photos	Archive them with the record of the patient they belong to.
Issued invoices	Keep them in the program or the archive where they were issued.

Step 2: ask your current provider for the export

Ask your current provider for a complete export in a common format, such as CSV or Excel, and ask exactly what it includes: whether all patients come out or only active ones, whether appointments carry the practitioner and room, and what format the medical records and documents come in.

If your current program is in the cloud, its provider processes your patients' data on behalf of the clinic. Under Article 28 of the GDPR, the contract with a data processor must stipulate that the processor, “at the choice of the controller, deletes or returns all the personal data to the controller after the end of the provision of services relating to processing”. The order matters: ask first for the complete return, check that you have it, and only then request deletion.

What you do not plan to migrate cannot be lost either. Spain's Ley 41/2002 (the basic law on patient autonomy and clinical documentation) requires healthcare centres to keep clinical documentation, though not necessarily on its original medium, for the period appropriate to each case and, as a minimum, five years from the date of discharge of each episode of care. And the archive must guarantee security, proper preservation and retrieval of the information.

Step 3: clean up before importing

An export covering years of work contains all sorts of things. Before importing it, spend a little time reviewing it in a spreadsheet:

• Duplicates. The same patient registered twice with the name spelt differently.
• ID numbers. Spanish DNI numbers with and without the letter, with dots or spaces, NIE numbers mixed in.
• Dates. Different formats in the same column, or impossible dates of birth.
• Phone numbers and emails. Prefixes, spaces and emails with obvious errors.
• Practitioner and room names. They must match the ones you will set up in the new program so that appointments land in the right place.

Always work on a copy of the file and keep the original untouched. And since this is health data, do not send it by unprotected email or leave it in a shared folder with people who do not need it.

Step 4: test with a copy

The first import should be a test, not the final one. Before touching anything, the new program should show you what is going to come in, what clashes with what is already there, and what is missing.

In Mi Clínica, importing patients and appointments works like this:

• It reads the CSV or Excel file and recognises the columns even if they are named differently; if an essential column is missing, the preview says so, so you can fix the file, and columns it does not recognise are not imported.
• The preview counts how many patients or appointments come in as new, how many are updated and how many are linked to an existing record with the same DNI, and shows row by row what does not come in, along with any warnings.
• A preview that is not run expires after one day: to import, you have to upload the file again.
• Importing the same file again does not duplicate anything. If an item has already been edited in Mi Clínica, the new import only fills gaps and never overwrites it.
• Every import can be undone: what it created is left inactive (patients) or cancelled (appointments), except anything edited afterwards or that already has activity of its own, such as an invoice or a progress note, and the program tells you why.

If you would rather not do it yourself, ask us to bring in your patients and appointments and we will do it for you.

Step 5: overlap and cut-over date

Pick a cut-over date: from that day on, new appointments are booked only in the new program. Until then, and for a few weeks afterwards, leave the old program open in read-only mode so you can look up old records and documents.

• Do the final import as close as possible to the cut-over date, so that future appointments are up to date.
• Check a sample by hand: ten random patients and the first week of the diary.
• Train the team with real cases before the first day, not during it.
• Do not cancel the old program until you hold the complete export, saved and checked.

The new provider is a processor too

The new program is going to hold health data on behalf of the clinic, so its provider is also a data processor. Article 28 of the GDPR requires you to use only a processor that provides sufficient guarantees, and to govern the relationship with a contract that sets out the subject matter, duration, nature and purpose of the processing. Sign it before importing the first patient.

Spain's LOPDGDD also clarifies that a processor's access to the data needed to provide the service is not considered a disclosure of data, provided the GDPR and the act itself are complied with.

What Mi Clínica imports and what it does not

Today Mi Clínica imports patients and appointments. Medical records, documents and invoices from another program are not imported yet: if you switch to Mi Clínica, that part is kept in the previous program's export, organised so it can be consulted. It is better to know this before you decide than to discover it on the day of the switch. If you are comparing options, also read what clinic management software should have.

Sources consulted

Checked on 12 October 2026. We link to the original source so that you can consult the current text.

• Reglamento (UE) 2016/679, Reglamento general de protección de datos. BOE (DOUE).
• Ley 41/2002, básica reguladora de la autonomía del paciente (texto consolidado). BOE.
• Ley Orgánica 3/2018, de Protección de Datos Personales y garantía de los derechos digitales (texto consolidado). BOE.