A method for authenticating an instrument for processing a biological sample or reagent is disclosed. The method comprises generating a PIN code by the instrument, entering the PIN code and identification data associated with the instrument in a database of an electronic device, verifying the PIN code and identification data at the electronic device, transmitting an authentication certificate to the instrument if the PIN code and identification data correspond to target data stored in the database, installing the authentication certificate on the instrument, whereby the instrument is registered with the electronic device, and using the authentication certificate for an encrypted communication between the instrument and the electronic device. Further, a system is disclosed which comprises an instrument for processing a biological sample or reagent and an electronic device. The system is configured to carry out each step of the method.