Background: Cognitive biases seem to play an important role in the development and maintenance of emotional disorders such as depression and anxiety. Novel procedures, known as Cognitive Bias Modification (CBM), aim to reduce these dysfunctional information processing modes. This study develops a brief online intervention program to modify biased interpretations in depression and anxiety, overcoming some methodological issues that have been addressed in previous literature. Methods: Volunteer participants will be recruited via social media, posters and universities. They will be randomly assigned to an experimental group or a waiting list control group. Both groups will attend two assessment sessions at the lab. The assessments will consist of questionnaires measuring cognitive and emotional variables as well as three experimental tasks to measure cognitive biases (i.e., attention, memory and interpretation). After the first assessment session, only participants in the experimental group will receive a link to follow the four-sessions program at home. All participants will receive, via email, follow-up questionnaires two weeks and three months after the second assessment session.Discussion: This study will test an online program potentially beneficial to modify cognitive variables in disorders such as depression and anxiety. Several limitations of previous CBM procedures are addressed and the impact of the program both on cognitive performance and clinical symptoms will be explored.Trial registration: This trial was prospectively registered on June 17, 2019 with the ClinicalTrials.gov NCT03987477