The use of eye tracking technology, together with other physiological measurements such as psychogalvanic skin response (GSR) and electroencephalographic (EEG) recordings, provides researchers with information about users’ physiological behavioural responses during their learning process in different types of tasks. These devices produce a large volume of data. However, in order to analyse these records, researchers have to process and analyse them using complex statistical and/or machine learning techniques (supervised or unsupervised) that are usually not incorporated into the devices. The objectives of this study were (1) to propose a procedure for processing the extracted data; (2) to address the potential technical challenges and difficulties in processing logs in integrated multichannel technology; and (3) to offer solutions for automating data processing and analysis. A Notebook in Jupyter is proposed with the steps for importing and processing data, as well as for using supervised and unsupervised machine learning algorithms.