Transfer data from Front Desk to Cliniko

Transfer your clinic data from Front Desk into Cliniko.

Marcus avatar
Written by Marcus
Updated over a week ago

If you're switching to Cliniko from Front Desk, then here are the details you’ll need in order to transfer your data into your Cliniko account!

Please note that this data transfer service is a process that we will work on with you—not something that you'll need to do yourself. Please don't import spreadsheets or manually add any information into your Cliniko account before the transfer, as duplication will result when your data comes across from Front Desk.

The very first step is booking your transfer date! We sometimes book months in advance, so we strongly recommend you book as soon as you can to avoid further delays:

Once you've done that, please read through the guide below. It's important to review each section thoroughly, as it outlines your role in the transfer, and what we do for you.

The guide is broken into the following sections:

Getting familiar with Cliniko

For a smooth transition, please ensure that your team has had an opportunity to play around with Cliniko and are familiar with it. The trial is unrestricted, so all features are available to set up and become familiar with. You can change your subscription level as required while trialing, which will let you add more practitioners!

In case it's useful, these training guides might come in handy:

All of our support articles and guides can be found on our help site, too! You can quickly search for anything you’d like help with right here.

All users are encouraged to contact our support team with any questions. We're easiest reached from within Cliniko by clicking Help on the blue sidebar, and clicking Chat with us! If you'd prefer email, you can reach us at

Organise decryption and export with Smartsoft

Your Front Desk account contains encrypted and non-encrypted data. The data is encrypted for patient privacy and protection, but this means that only the Front Desk application is able to read that information. Decrypting this data ensures that Cliniko is able to read it and transfer it into your Cliniko account.

Only patient treatment notes and attached files are encrypted. If you do not have any of this data stored in Front Desk, or you do not want to transfer that data, then there is no need to engage Smartsoft to perform the decryption service for you. You can simply perform your own backup of your data. Here's Smartsoft's instructions on doing that:

If you do have treatment notes and attached files, and you need them transferred to Cliniko, Smartsoft will perform an in-place decryption of this data in your Front Desk database. Contact Smartsoft support or your Front Desk account manager to organise this. Please note that decryption of your Front Desk database is a billable service by Smartsoft. You will need to request a quote for this service.

Note that any data entered into Front Desk after this decryption and backup will not be transferred to Cliniko, as it won't be included in the database backup supplied to us. This data will need to be noted and manually entered into Cliniko after the transfer has been completed.

In some cases, if your Front Desk database is quite large, Smartsoft may need to perform a FILESTREAM upgrade to support the additional volume of unencrypted data. This is also a billable service by Smartsoft.

In case it helps, here's a pro-forma that you may wish send to Smartsoft to organise transfer:

Dear Smartsoft,

We are planning to move our practice to another system, and are organising to migrate our Front Desk data as part of that move.

This process involves migrating Clinical Notes and Attachments, which we understand are encrypted in our Front Desk database. In order to export these, we'll need you to perform an in-place decryption of this data. Could you please provide us a quote for this work, and indicate when your team will be available to do this?

In addition, you may need to perform a Filestream upgrade to SQL Express if our decrypted database size will exceed 10GB, so please could you factor this in, and perhaps arrange a review of our system prior to then?

Kind regards,

Your Front Desk backup is likely to be very large—generally between 2GB and 200GB, depending on your volume of patients, attachments, clinical notes, and so forth. The decryption process may take some time.

Once your decryption and back-up has completed, you should have two files as a result - one named FD.bak, and a much larger one named something like FD_DECRYPTED.bak. The decrypted one is the one we need. Please compress it by right-clicking the file, selecting Send to... then select Compressed (zipped) folder.

Once you have your decrypted and zipped database file, please upload it to your preferred cloud storage service (Microsoft OneDrive, Google Drive, Dropbox, etc), and create a share link to provide to us. Contact us if you need any help with this.

At a minimum, please schedule your decryption and backup for one to two days before your scheduled transfer, and upload it to your chosen storage option by the day before your scheduled transfer. It's important to have all these steps completed prior to the transfer to avoid delays, as we still require time on the day of transfer to load and prepare your data in our system to then be written into your Cliniko account.

🚨 IMPORTANT: If you have more than 10 years or 10,000 patients of data to transfer, please let us know. This is absolutely fine, but the transfer may take more than a day, and extra allowances will need to be made for this volume of data.

Setting up your Cliniko account

There's a bit of setup required in Cliniko prior to the transfer. These are things that we can't necessarily determine or transfer from Front Desk, or settings that are specific to Cliniko.

Please ensure the following things are set up as soon as possible:

  1. All required users and practitioners are created,

  2. All sites/locations of your business are set up as Cliniko business locations,

  3. Your time zones have been set correctly (to ensure that appointments get transferred to the right spots), and

  4. Mobile phone numbers have been added to the admin user's account so that we can authenticate prior to transfer.

Other items that are not required prior to transfer, but are not transferred and will need to be set up manually are:

  1. All treatment note templates are created,

  2. All letter templates are created,

Past practitioners

Note that when we transfer appointments, we will need a practitioner assigned to the appointment. This is a little complicated for instances where the practitioner is no longer with you and therefore not in Cliniko. In these cases, please let us know whether you would prefer to assign the appointments to:

  • A generic ‘Former practitioner’ that you create in Cliniko,

  • Another active practitioner in Cliniko, or

  • Exclude them entirely.

Alternatively, you may create all your specific members of staff (past and present) in Cliniko, and we’ll assign all appointments correctly. You can set those former practitioners as inactive, as your Cliniko subscription price is based on the total number of active practitioners.

File attachments

Finally, Cliniko limits the volume of patient attachments in trial accounts. To remove this limit, please add your billing details into your account. Your free trial will continue until completion, and your credit card will not be charged until your trial period has expired.

You can quickly search for and find our guides and help articles to assist you with the setup process on our help site, here.

If you'd like any assistance with getting set up, feel free to contact us! Even if you just have a quick question that you’d like an answer for, we are easiest reached from within Cliniko by clicking Help on the blue sidebar, and clicking Chat with us! You can also click the chat "bubble" at the bottom right corner of this page.

What do we transfer?

Note that no data is removed from Front Desk in the transfer process. Data is copied to your Cliniko account. The types of data that are transferred are not customisable.

Transfer to Cliniko will include the following from your Front Desk database, and will appear as described in Cliniko:

  • Products

  • Services (billable items in Cliniko)

  • Appointment types

  • Suppliers and referrers (contacts in Cliniko)

  • Clients and archived/inactive clients

  • Referring GPs (contacts in Cliniko)

  • Appointments (historical and future) and attendance status (arrived, DNA, cancelled)

  • Clinical notes (plain text treatment notes in Cliniko - most formatting is lost during transfer. Where a clinical note contains images, it will become a PDF file attachment to the patient)

  • Patient warnings and reminders

  • Patient attachments (patient files in Cliniko)

  • X-rays and supporting reports (patient files in Cliniko, as either images for x-rays without reports, or PDF files for x-rays with reports)

  • Patient letters (converted to plain text PDF patient files in Cliniko. Formatting and images will be lost)

Transfers can take anywhere from a few hours to a day, depending on the volume of data being transferred.

Once we’ve finished transfer, you will need to review your appointment types within Cliniko and finish setting them up (assign practitioners to them, assign colours, relate billable items and treatment note templates, assign reminder and confirmation templates).

Prior to the data transfer, please avoid creating or performing any data imports for:

  • Patients

  • Products

  • Contacts

  • Appointment types

  • Billable items

We will import all of these as part of the Front Desk transfer. If that data is already in Cliniko, it will be duplicated.

What don’t we transfer?

Unfortunately, all financial details are excluded from transfer. There is not a way to import financial data into Cliniko. This includes:

  • Invoices

  • Payments

  • Credits

  • Account statements

  • Appointment invoice/payment statuses

If you'd like to record prior payment history or outstanding debts in Cliniko, you can create an opening balance for those patients. This is not considered revenue and will not affect Cliniko's reporting.

In addition, the following items are not transferrable and must be set up manually where needed:

  • Users and practitioners, practitioner reference numbers

  • Businesses locations and settings

  • Expenses and stock sales

  • 3rd party app integrations

  • Communication records

  • Waitlist data

  • Existing reports

  • Letters and letter templates

  • Patient forms and form templates

  • Communication templates (email and SMS)

Information that we need from you

When you book a transfer date, you'll be sent a confirmation email which includes a link to a secure electronic form. This form is where the below information is collected from you. If you miss the confirmation email, another link to the same form will be sent in a reminder email closer to your transfer date. Please let us know if you do not receive these emails.

The following are some questions we need to know to accurately transfer data into Cliniko. If you're unsure of the answer, please seek clarification.

How many sites/locations do you practice at, and are all of these sites in the Front Desk calendar?

Do you use Practice Groups in Front Desk?
If so, do you use them to represent locations? If not, how do you represent different locations?

Do you use Charge Types/Fee Categories in Front Desk?
If so, do these represent concessional pricing for the type of patient (e.g. Student, Senior, etc.), or tiered practitioner pricing for the type of practitioner (e.g. Junior, Senior, Associate, etc.)?

Are your patient warnings confidential? (These are the warnings displayed when opening a patient file.)

If they are not confidential, we'll store them against the patient visible to all members of staff. If they are confidential, we'll store them as confidential medical alerts visible only to practitioners and administrators in Cliniko.

Do you use casual appointments?

If so, do you use them to represent calendar notes, or walk-in appointments? If neither, what do you use them for?

Do you have any practitioners in Front Desk who are inactive?
If so, we will need to determine what to do with appointments assigned to them. There are a couple of options here:

  1. We can leave those appointments behind and not transfer them into Cliniko.

  2. You can create all your inactive practitioners in Cliniko, and we can assign appointments to the correct practitioner. You can make these practitioners inactive in Cliniko prior to transfer, so they do not contribute to your subscription plan.

  3. You can elect one or more other practitioners in Cliniko to assign those appointments to (e.g. use an existing practitioner, or create one practitioner named “Old Front Desk practitioner”, or similar). You'll just need to tell us which practitioner/s in Front Desk you want mapped to which practitioner/s in Cliniko.

Accessing your Cliniko account

In order to access your new Cliniko account and write your data to it, we’ll need your Cliniko URL and an API key. When you book a transfer date, you'll be sent a confirmation email which includes a link to a secure electronic form. This form is where this information is collected from you. If you miss the confirmation email, another link to the same form will be sent in a reminder email closer to your transfer date. Please let us know if you do not receive these emails.

Cliniko URL

Your URL can be found in your browser address bar when you're logged in to Cliniko, and will look something like This is required so that we may be sure we’re transferring data to the correct account.

Cliniko API key

Please log in to your Cliniko account to generate the API key. You'll need to be logged in as an administrative user who is also a practitioner so that the API key generated has the required data access permissions. Please also see our guide on generating a Cliniko API key.

To have the correct permissions, the API key must belong to a user who is also a practitioner. Please do not give us an API key for an administrator that is not also a practitioner.

Your API keys are like passwords, and must be handled with care. It's very important that this information is transmitted to us securely. When you book a transfer date, you'll be sent a confirmation email which includes a link to a secure electronic form. This form is where you can safely communicate your API keys and other information to us. If you miss the confirmation email, another link to the same form will be sent in a reminder email closer to your transfer date. Please let us know if you do not receive these emails.

Administrator mobile numbers

We’ll also need to do some verification of an account administrator to get the final go-ahead to access the account and load data, so please ensure a mobile numbers are included in user's profiles so we can send a verification code to the required user.

On the day of the transfer

As a reminder, uploading your Front Desk backup will take time, and transfer into Cliniko cannot start until that backup is uploaded to us. If this process is only able to start on the morning of transfer, your actual transfer may not commence until much later in the day. Accordingly, please schedule decryption and upload to be completed by the day prior to your transfer.

We shouldn’t need to hassle you much on the day of the transfer, unless some of the above information or setup is missing, so please ensure you are contactable on the day. We’ll get started in the morning (AEDT) and let you know when we are done! If it looks like things will take longer than the day, we’ll be sure to reach out and keep you informed of the progress.

When the transfer is completed, you’ll be able to use your data within Cliniko immediately.

If there’s anything you’d like to confirm or discuss prior to transfer, please do let us know—we’re here to help!

The final checklist

Having all of this done before the transfer takes place is super important. Please be sure that each item on these lists has been checked off prior to your transfer date!

Please be sure that you have completed the following:

  • The transfer date has been booked

  • Decryption and backup of database has been arranged with Smartsoft if required

  • Your Front Desk database has been zipped, uploaded to your your chosen online storage, and a share link given to the Cliniko team

  • Completed the secure form to give us your Cliniko URL and API key (see instructions), and the answers to your questions (see questions)

On the Cliniko side of things:

  • [Required] Practitioners have been created, both active and inactive (see guide)

  • [Strongly recommended] All administrator user accounts have mobile numbers

  • [Required] Business locations have been created, both active and inactive (see guide)

  • [Required] You have added a payment method to your Cliniko subscription, to lift the file upload limitation (see guide)

After transfer, these items will need attending to:

  • Ensure all required appointments types are created (see guide)

  • Set practitioners as providers of appointment types (see guide)

  • Create treatment note templates (see guide)

  • Create letter templates (see guide)

  • Create billable items (see guide)

  • Relate billable items to appointment types (see guide)

  • Relate treatment note templates to appointment types (see guide)

We know that transferring from another system is a big deal, and we want to help make the process as easy as possible for you. If you have any questions on anything at all, please reach out to us. We're always available to help!

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