Research has established the effect of emotions on academic performance and on development of autonomy in undergraduate students in the virtual modality, based on a mixed study with descriptive approach performed in three Higher Education Institutions in Colombia. This study consulted 1,628 students, as follows: freshmen (first semester), in fourth and fifth semesters, and seniors (seventh, eighth and ninth semester). The study regarded the variable duration of each program (between eight and ten semesters) in each institution. The data for each group of students was collected simultaneously. Research results evinced that academic performance and development of autonomy, overall, are affected by emotions, specifically by the lack of control of mood, frustration, fear of expressing ideas and disillusion with learning results, largely because it entails self-control, establishing good interpersonal relationships and assertive communication.